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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/2457?offset=10</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/27225/painless-package-development-for-r</guid>
	<pubDate>Tue, 03 May 2016 05:31:06 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/27225/painless-package-development-for-r</link>
	<title><![CDATA[Painless package development for R]]></title>
	<description><![CDATA[<p>Devtools makes package development a breeze: it works with R&rsquo;s existing conventions for code structure, adding efficient tools to support the cycle of package development. With devtools, developing a package becomes so easy that it will be your default layout whenever you&rsquo;re writing a significant amount of code.</p>
<p>Before you get started be sure to check out:</p>
<ul>
<li><a href="https://groups.google.com/forum/#%21forum/rdevtools" title="Google devtools Group">devtools Google Group &ndash;&nbsp;https://groups.google.com/forum/#!forum/rdevtools</a></li>
<li><a href="http://adv-r.had.co.nz/" title="Hadley W Online Book">book on &ldquo;Advanced R programming&rdquo; &ndash;&nbsp;http://adv-r.had.co.nz/</a></li>
<li><a href="https://github.com/hadley/devtools" title="devtools GitHub">GitHub repository &ndash;&nbsp;https://github.com/hadley/devtools</a></li>
</ul>
<h3 id="getting_started">&nbsp;</h3><p>Address of the bookmark: <a href="https://www.rstudio.com/products/rpackages/devtools/" rel="nofollow">https://www.rstudio.com/products/rpackages/devtools/</a></p>]]></description>
	<dc:creator>Abhi</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29635/r-graphs</guid>
	<pubDate>Fri, 04 Nov 2016 10:48:00 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29635/r-graphs</link>
	<title><![CDATA[R Graphs !!]]></title>
	<description><![CDATA[<p><span>The blog is a collection of script examples with example data and output plots. R produce excellent quality graphs for data analysis, science and business presentation, publications and other purposes. Self-help codes and examples are provided. Enjoy nice graphs !!</span></p><p>Address of the bookmark: <a href="http://rgraphgallery.blogspot.be/" rel="nofollow">http://rgraphgallery.blogspot.be/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32152/upsetr-shiny-app</guid>
	<pubDate>Fri, 14 Apr 2017 06:19:54 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32152/upsetr-shiny-app</link>
	<title><![CDATA[UpSetR Shiny App!]]></title>
	<description><![CDATA[<p>UpSetR generates static&nbsp;<a href="http://vcg.github.io/upset/?dataset=0&amp;duration=1000&amp;orderBy=subsetSize&amp;grouping=groupByIntersectionSize&amp;selection=">UpSet plots</a>. The UpSet technique visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such as the number of elements in the aggregates and intersections, as well as additional summary statistics derived from subset or element attributes.</p>
<h4>To begin, input your data using one of the three input styles.</h4>
<ol>
<li>"File" takes a correctly formatted.csv file.</li>
<li>"List" takes up to 6 different lists that contain unique elements, similar to that used in the web applications BioVenn&nbsp;<a href="http://www.biomedcentral.com/content/pdf/1471-2164-9-488.pdf">(Hulsen et al., 2008)</a>&nbsp;and jvenn&nbsp;<a href="http://www.biomedcentral.com/content/pdf/1471-2105-15-293.pdf">(Bardou et al., 2014)</a></li>
<li>"Expression" takes the input used by the venneuler R package&nbsp;<a href="https://cran.r-project.org/web/packages/venneuler/venneuler.pdf">(Wilkinson, 2015)</a></li>
</ol><p>Address of the bookmark: <a href="https://gehlenborglab.shinyapps.io/upsetr/" rel="nofollow">https://gehlenborglab.shinyapps.io/upsetr/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/918/data-mining-in-bioinformatics</guid>
	<pubDate>Tue, 16 Jul 2013 03:21:28 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/918/data-mining-in-bioinformatics</link>
	<title><![CDATA[Data Mining in Bioinformatics]]></title>
	<description><![CDATA[<p>Data mining, the extraction of hidden predictive information from large databases. Data mining is becoming an increasingly important tool to transform this data into information. It is commonly used in a wide range of profiling practices, such as marketing, surveillance, fraud detection and scientific discovery. Data Mining for Bioinformatics enables researchers to meet the challenge of mining vast amounts of biomolecular data to discover real knowledge. In other words, you&rsquo;re a bioinformatician, and data has been dumped in your lap. Find the patterns, trend, answers, or what ever meaningful knowledge the data is hiding. They scour databases for hidden patterns, finding predictive information that experts may miss because it lies outside their expectations.This page Covering theory, algorithms, and methodologies, as well as data mining technologies. Unfortunately life is never simple. In molecular biology, it&rsquo;s becoming more common to generate reams of data then ask someone in bioinformatics to produce an answer. This is exploratory data analysis, one of the most difficult things to do well. Especially if you&rsquo;re thrown in at the deep end.</p><p><strong>Data mining commonly involves four classes of tasks:</strong></p><ul>
<li>Classification - Arranges the data into predefined groups. For example, an email program might attempt to classify an email as legitimate or spam. Common algorithms include decision tree learning, nearest neighbor, naive Bayesian classification and neural networks.</li>
<li>Clustering - Is like classification but the groups are not predefined, so the algorithm will try to group similar items together.</li>
<li>Regression - Attempts to find a function which models the data with the least error.</li>
<li>Association rule learning - Searches for relationships between variables. For example a supermarket might gather data on customer purchasing habits. Using association rule learning, the supermarket can determine which products are frequently bought together and use this information for marketing purposes. This is sometimes referred to as market basket analysis.</li>
<li>From experience, I can say that is one of the most frustrating positions to be in. Data mining is a huge field and can easily be bewildering for a beginner. However, high through-put techniques in molecular biology require, more and more, that bioinformatics is required to interpret the data. Furthermore, people working in bioinformatics generally come from computer science, or biology backgrounds. Data mining, however, involves statistics to one degree or another, which means entering a field that is may not be your strong point.</li>
<li>Excel is fine for creating graphs. If you&rsquo;re serious about data mining though, you&rsquo;ll need something more heavy weight. I use R, free, and with good data mining packages such as vegan and labdsv. For beginners R can be impenetrable, I recommend this book an introduction to R as well as the underlying statistics.</li>
<li>Any of us can rush head on into a land of support vector machines, hidden markov models and neural networks. But coming back to the first point, what are you trying to prove? Always question what are you doing, how does it fit in to the wider picture? Try to regularly review, and keep track of where you are going? This will prevent you from falling into data mining despair.</li>
</ul><p><strong>Data Mining Resources on the net:</strong><br /><br />A laboratory of data mining and bioinformatics is headed by Prof. Ambuj Singh. There are currently seven graduate students in the research group. Our research focuses on image informatics and scalable querying and mining of graphs.For more detail visit:&nbsp;<a href="http://www.cs.ucsb.edu/~dbl/">http://www.cs.ucsb.edu/~dbl/</a></p><p>Here are the materials (Lecture notes) from several past courses on data mining and/or Web mining by Stanford: For detail visit:&nbsp;<a href="http://infolab.stanford.edu/~ullman/mining/mining.html">http://infolab.stanford.edu/~ullman/mining/mining.html</a><br />Statistical Data Mining Tutorial Slides by Andrew Moore The following links point to a set of tutorials on many aspects of statistical data mining, including the foundations of probability, the foundations of statistical data analysis, and most of the classic machine learning and data mining algorithms. For detail visit:&nbsp;<a href="http://www.autonlab.org/tutorials/">http://www.autonlab.org/tutorials/</a></p><p>A tutorial on Introduction to Data Mining for Discovering hidden value in your data warehouse:<a href="http://www.thearling.com/text/dmwhite/dmwhite.htm">http://www.thearling.com/text/dmwhite/dmwhite.htm</a>&nbsp;<br />Wiki Links:&nbsp;<a href="http://en.wikipedia.org/wiki/Data_mining">http://en.wikipedia.org/wiki/Data_mining</a><br />Bioinformatics with Clementine&nbsp;<a href="http://www.spss.ch/upload/1051192224_inseratClemBio.pdf">http://www.spss.ch/upload/1051192224_inseratClemBio.pdf</a>&nbsp;<br />Causal Data Mining in Bioinformatics by Ioannis Tsamardinos:&nbsp;<a href="http://www.forth.gr/ics/bmi/In_the_News/2007/EN69-4.pdf">http://www.forth.gr/ics/bmi/In_the_News/2007/EN69-4.pdf</a></p><p>Report on ACM Text Mining in Bioinformatics (TMBIO 006)&nbsp;<a href="http://www.sigir.org/forum/2007J/2007j_sigirforum_song.pdf">http://www.sigir.org/forum/2007J/2007j_sigirforum_song.pdf</a>&nbsp;<br />BIOKDD 2002: Recent Advances in Data Mining for&nbsp;<br />Bioinformatics:&nbsp;<a href="http://www.acm.org/sigs/sigkdd/explorations/issue4-2/zaki.pdf">http://www.acm.org/sigs/sigkdd/explorations/issue4-2/zaki.pdf</a></p><p><strong>Bioinformatics and Medical Informatics:</strong>&nbsp;<br /><br />Tools for Mining and Applying Genetic Information in Patient Care:<a href="http://www.biomedtechalliance.org/pdfs/03_03_05/03_03_05.pdf">http://www.biomedtechalliance.org/pdfs/03_03_05/03_03_05.pdf</a></p><p>DATA MINING OF MICROARRAY DATABASES FOR HUMAN LUNG CANCER:&nbsp;<a href="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.106.385&amp;rep=rep1&amp;type=pdf">http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.106.385&amp;rep=rep1&amp;type=pdf</a></p><p>Towards knowledge-based gene expression data mining:&nbsp;<a href="http://www.ailab.si/blaz/papers/2007-JBI-BellazziZupan.pdf">http://www.ailab.si/blaz/papers/2007-JBI-BellazziZupan.pdf</a></p><p>DRAFT Accepted for publication in 'Data Mining in Bioinformatics'<br />Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Springer:<a href="http://www.cs.helsinki.fi/u/htoivone/pubs/gene_mapping_by_pattern_discovery.pdf">http://www.cs.helsinki.fi/u/htoivone/pubs/gene_mapping_by_pattern_discovery.pdf</a></p><p>Data Mining and Text Mining for Bioinformatics: Proceedings of the European Workshop:&nbsp;<a href="http://www.rok.informatik.hu-berlin.de/wbi/research/publications/2003/proceedings_ws_mining.pdf">http://www.rok.informatik.hu-berlin.de/wbi/research/publications/2003/proceedings_ws_mining.pdf</a></p><p><strong>Biological Network Analysis:<br /></strong><br />Graph Mining in Bioinformatics:&nbsp;<a href="http://agbs.kyb.tuebingen.mpg.de/wikis/bg/BNA-5.pdf">http://agbs.kyb.tuebingen.mpg.de/wikis/bg/BNA-5.pdf</a>.</p><p>Text mining in bioinformatics:&nbsp;<a href="http://agbs.kyb.tuebingen.mpg.de/wikis/bg/4.pdf">http://agbs.kyb.tuebingen.mpg.de/wikis/bg/4.pdf</a></p><p>Some datamining books that are available on google books:</p><p>Data mining and bioinformatics: first international workshop, VDMB 2006 By Mehmet M. Dalkilic</p><p>Data mining: concepts and techniques By Jiawei Han, Micheline Kamber</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/1720/postdoctoral-associate-bioinformatics-at-duke-university-medical-center</guid>
  <pubDate>Sat, 10 Aug 2013 18:38:38 -0500</pubDate>
  <link></link>
  <title><![CDATA[Postdoctoral Associate - Bioinformatics  at Duke University Medical Center]]></title>
  <description><![CDATA[
<p>The Department of Biostatistics and Bioinformatics at Duke University Medical Center is seeking a Postdoctoral Associate for a one year appointment to work on several high-dimensional research projects. The specific goals of the project are to identify genes or molecular markers that are predictive of clinical outcomes in renal and prostate cancer.</p>

<p>Candidates must have: a PhD degree in statistics, biostatistics or bioinformatics, extensive experience in analyzing high-dimensional data (microarray, SNP, CNVs) and of validation approaches. In addition, experience in penalized regression methods, data base manipulation; and strong programming skills in order to conduct Monte Carlo studies and applications (R). Candidate must have excellent communication skills (verbal, written and presentation), a strong proficiency in Linux system.</p>

<p>This position is available immediately and will be filled as soon as possible. Appointment could be extended beyond the first year based on additional funding.</p>

<p>For more information about the Department of Biostatistics and Bioinformatics, please visit our website: http://www.biostat.duke.edu.</p>

<p>For more info: http://biostat.duke.edu/sites/biostat.duke.edu/files/Halabi%20-%20Postdoc%20Job%20Posting%202013%20updated.pdf</p>

<p>Duke University is an Equal Opportunity/Affirmative Action Employer.</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/2261/best-book-titles-for-learning-bionformatics</guid>
	<pubDate>Tue, 13 Aug 2013 17:31:51 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/2261/best-book-titles-for-learning-bionformatics</link>
	<title><![CDATA[Best book Titles for Learning Bionformatics]]></title>
	<description><![CDATA[<p>Nothing can add to our intellect more than reading a book. &nbsp;In books, we can experience new things that we would not normally be able to experience. It is proved that books can change our lives and other people&rsquo;s lives. Reading can make us more intelligent, updated, imaginative. Without reading we wouldn&rsquo;t know anything that we know today. There are several book, online and offile to read and I can't mentioned all of them here in the list. Therefore, I mentioned some bioinformatics and its related books in subgroups. Hope you will like the list.&nbsp;</p><p>Sequence Analysis and General Bioinformatics</p><ul>
<li>BLAST, Ian Korf, Mark Yandell, Joseph Bedell, 2003, O'Reilly</li>
<li>Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases, Scott Markel, Darryl Leon, 2003, O'Reilly</li>
<li>Bioinformatics for Geneticists, Michael Barnes, Ian C Gray (Editors), 2003, John Wiley &amp; Sons</li>
<li>Bioinformatics for Dummies, Jean-Michel Claverie, Cedric Notredame, 2003, John Wiley &amp; Sons</li>
<li>Mathematics of Genome Analysis, Jerome K. Percus, 2002, Cambridge Univ Press</li>
<li>Bioinformatics Computing, Bryan P. Bergeron, 2002, Prentice Hall</li>
<li>Evolutionary Computation in Bioinformatics, Gary B. Fogel, David W. Corne (Editors), 2002, Morgan Kaufmann</li>
<li>Introduction to Bioinformatics, Arthur M. Lesk, 2002, Oxford University Press</li>
<li>Instant Notes in Bioinformatics, D.R. Westhead, J. H. Parish, R.M. Twyman, 2002, Bios Scientific Pub</li>
<li>Fundamental Concepts of Bioinformatics, Dan E. Krane, Michael L. Raymer, Michaeel L. Raymer, Elaine Nicpon Marieb, 2002, Benjamin/Cummings</li>
<li>Essentials of Genomics and Bioinformatics, C. W. Sensen (Editor), 2002, John Wiley &amp; Sons</li>
<li>Current Topics in Computational Molecular Biology (Computational Molecular Biology), Tao Jiang, Ying Xu, Michael Zhang (Editors), 2002, MIT Press</li>
<li>Hidden Markov Models for Bioinformatics, Timo Koski, Timo Koskinen, 2001, Kluwer Academic Publishers</li>
<li>Bioinformatics: From Genomes to Drugs, Thomas Lengauer (Editor), 2001, John Wiley &amp; Sons</li>
<li>Statistical Methods in Bioinformatics: An Introduction (Statistics for Biology and Health), Warren Ewens, Gregory Grant, 2001, Springer Verlag</li>
<li>Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition, Andreas D. Baxevanis, B. F. Francis Ouellette, 2001, Wiley-Interscience</li>
<li>Bioinformatics: The Machine Learning Approach, Second Edition (Adaptive Computation and Machine Learning), Pierre Baldi, Soren Brunak, Sren Brunak, 2001, MIT Press</li>
<li>Introduction to Bioinformatics, T eresa Attwood, David Parry-Smith, 2001, Prentice Hall</li>
<li>Bioinformatics: A Primer, Charles Staben, 2001, Jones &amp; Bartlett Pub</li>
<li>Data Analysis and Classification for Bioinformatics, Arun Jagota, 2000, AKJ Academics</li>
<li>Bioinformatics: Sequence and Genome Analysis, David W. Mount, 2001, Cold Spring Harbor Laboratory Press</li>
<li>Bioinformatics: A Biologist's Guide to Biocomputing and the Internet, Stuart M. Brown, 2000, Eaton Pub Co</li>
<li>Bioinformatics: Sequence, Structure and Databanks: A Practical Approach (The Practical Approach Series, 236), Des Higgins (Editor), Willie Taylor (Editor), 2000, Oxford Univ Press</li>
<li>Neural Networks and Genome Informatics, Cathy H. Wu, Jerry W. McLarty, 2000, Elsevier Science</li>
<li>Computational Molecular Biology: An Introduction (Wiley Series in Mathematical and Computational Biology), Peter Clote and Rolf Backofen, 2000, John Wiley &amp; Sons</li>
<li>Computational Molecular Biology: An Algorithmic Approach, Pavel A. Pevzner, 2000, MIT Press</li>
<li>Post-Genome Informatics, Minoru Kanehisa, 2000, Oxford Univ Press</li>
<li>Mathematical and Computational Biology: Computational Morphogenesis, Hierarchical Complexity, and Digital Evolution, Chrystopher L. Nehaniv, 1999, American Mathematical Society</li>
<li>Pattern Discovery in Biomolecular Data: Tools, Techniques, and Applications, Jason T. L. Wang, Bruce A. Shapiro, Dennis Elliott Shasha (Editors), 1999, Oxford Univ Press</li>
<li>Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison, David Sankoff and Joseph Kruskal (Editors), 1999, Cambridge University Press</li>
<li>Bioinformatics Basics: Applications in Biological Science and Medicine, Hooman Rashidi, 1999, CRC Press</li>
<li>Bioinformatics: Methods and Protocols (Methods in Molecular Biology, Vol 132), Stephen Misener and Stephen A. Krawetz (Editors),1999, Humana Press</li>
<li>Bioinformatics: Databases and Systems, Stanley Letovsky (Editor),1999, Kluwer Academic Publishers</li>
<li>Computational Molecular Biology, P. Green, 1998, Blackwell Science Inc.</li>
<li>Computational Methods in Molecular Biology (New Comprehensive Biochemistry, V. 32), Steven L. Salzberg, David B. Searls, Simon Kasif (Editors), 1998, Elsevier Science Ltd.</li>
<li>Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Richard Durbin, S. Eddy, A. Krogh, G. Mitchison, 1998, Cambridge University Press</li>
<li>Guide to Human Genome Computing, M. J. Bishop (Editor), 1998, Academic Press</li>
<li>Introduction to Computational Molecular Biology, Joao Meidanis, Joao C. Setabal, 1997, PWS Pub. Co.</li>
<li>Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, Dan Gusfield, 1997, Cambridge University Press</li>
<li>Sequence Data Analysis Guidebook, Simon R. Swindell (Editor), 1997, Humana Press</li>
<li>High Performance Computational Methods for Biological Sequence Analysis, Tieng K. Yap, Ophir Frieder, Robert L. Martino, 1996, Kluwer Academic Pub.</li>
<li>Computer Methods for Macromolecular Sequence Analysis, Methods in Enzymology, volume 266, Russell F. Doolittle (Editor), 1996, Academic Press</li>
<li>DNA and Protein Sequence Analysis: A Practical Approach (Practical Approach Series , No 171), 1996, M. J. Bishop and C. J. Rawlings (Editors), 1996, IRL Press</li>
<li>Molecular Bioinformatics: Algorithms and Applications, Steffen Schulze-Kremer, 1995, Walter De Gruyter</li>
<li>Introduction to Computational Biology - Maps, sequences and genomes, Michael S. Waterman, 1995, Chapman &amp; Hall</li>
<li>Computer Analysis of Sequence Data, Annette M. Griffin and Hugh G. Griffin (Editors), 1994, Humana Press</li>
<li>Artificial Intelligence and Molecular Biology, Lawrence Hunter (Editor), 1993, AAAI Press</li>
<li>Sequence Analysis Primer, Michael Gribskov and John Devereux (Editors), 1992, Oxford University Press</li>
<li>Mathematical Methods of Analysis of Biopolymer Sequences (Dimacs Series in Discrete Mathematics and Theoretical Computer Science ; Volume 8), S. G. Gindikin, 1992, American Mathematical Society</li>
<li>Mathematical Methods for DNA Sequences, Michael S. Waterman (Editor), 1989, CRC Press</li>
</ul><p>Programming Books for Bioinformatics</p><ul>
<li>Mastering Perl for Bioinformatics, James D. Tisdall, 2003, O'Reilly</li>
<li>Genomic Perl: From Bioinformatics Basics to Working Code, Rex A. Dwyer, 2002, Cambridge University Press</li>
<li>Beginning Perl for Bioinformatics, James Tisdall, 2001, O'Reilly</li>
<li>Developing Bioinformatics Computer Skills, Cynthia Gibas, Per Jambeck, 2001, O'Reilly</li>
</ul><p>General Genomics</p><ul>
<li>Functional Microbial Genomics (Volume 33), Brendan Wren, Nick Dorrell, 2003, Academic Press</li>
<li>Discovering Genomics, Proteomics, and Bioinformatics, A. Malcolm Campbell, Laurie J. Heyer, 2002, Benjamin/Cummings</li>
<li>Genomes, Terence A. Brown, 2002, John Wiley &amp; Sons</li>
<li>Essentials of Medical Genomics, Stuart M. Brown , 2002, John Wiley &amp; Sons</li>
<li>A Primer of Genome Science, Greg Gibson, Spencer V. Muse, 2002, Sinauer Associates</li>
<li>Pathogen Genomics: Impact on Human Health, Karen Joy, Phd Shaw (Editors), 2002, Humana Press</li>
<li>Genomics, John E. Antonopoulos, 2000, Xlibris Corporation</li>
<li>Genomics and Proteomics: Functional and Computational Aspects, Sandor Suhai (Editor), 2000, Plenum Pub Corp</li>
<li>Functional Genomics: A Practical Approach (The Practical Approach Series, 235), S. Hunt and F. Livesey (Editors), 2000, Oxford Univ Press</li>
<li>Human Molecular Genetics, Andrew P. Read, Tom Strachan 1999, BIOS Scientific Publishers Ltd.</li>
<li>Genomics: The Science and Technology Behind the Human Genome Project, Charles R. Cantor and Cassandra L. Smith, 1999, John Wiley &amp; Sons</li>
<li>Cells: A Laboratory Manual, 3 volumes, David L. Spector, Robert D. Goldman, Leslie A. Leinwand, 1998, Cold Spring Harbor Laboratory Press</li>
<li>Genome Analysis: A Laboratory Manual, 4 volumes, Bruce Birren, et al. (Editors), 1997, Cold Spring Harbor Laboratory Press</li>
<li>The Human Genome Project, N. G. Cooper (Editor), 1994, University Science Books</li>
</ul><p>Comparative Genomics</p><ul>
<li>Handbook of Comparative Genomics: Principles and Methodology, Cecilia Saccone, Graziano Pesole, 2003, Wiley-Liss</li>
<li>Sequence - Evolution - Function: Computational Approaches in Comparative Genomics, Eugene V. Koonin, Michael Y. Galperin, 2002, Kluwer Academic Publishers</li>
<li>Comparative Genomics - Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families, David Sankoff and Joseph H. Nadeau, 2000, Kluwer Academic Pub</li>
<li>Comparative Genomics, Melody Clark (Editor), 2000, Kluwer Academic Pub</li>
</ul><p>Proteomics</p><ul>
<li>Proteins and Proteomics: A Laboratory Manual, Richard J. Simpson (Editor), Cold Spring Harbor Laboratory</li>
<li>Proteomics in Practice: A Laboratory Manual of Proteome Analysis , Reiner Westermeier, Tom Naven, 2002, John Wiley &amp; Sons</li>
<li>Posttranslational Modifications of Proteins: Tools for Functional Proteomics (Methods in Molecular Biology, Vol 194) , Christoph Kannicht (Editor), 2002, Humana Press</li>
<li>Peptide Arrays on Membrane Supports: Synthesis and Applications (Springer Lab Manual), Joachim Koch, Michael Mahler (Editors), 2002, Springer Verlag</li>
<li>Proteomics , Timothy Palzkill, 2002, Kluwer Academic Publishers</li>
<li>Introduction to Proteomics: Tools for the New Biology , Daniel C. Liebler (Editor), 2001, Humana Press</li>
<li>Proteome Research: Mass Spectrometry (Principles and Practice) , P. James (Editor), 2001, Springer Verlag</li>
<li>Interpreting Protein Mass Spectra: A Comprehensive Resource , A. Peter Snyder, 2000, American Chemical Society</li>
<li>Protein Sequencing and Identification Using Tandem Mass Spectrometry , Michael Kinter, Nicholas E. Sherman, 2000, Wiley-Interscience</li>
<li>From Genome to Proteome: Advances in the Practice and Application of Proteomics, Michael J. Dunn (Editor), 2000, Vch Verlagsgesellschaft Mbh</li>
<li>Proteomics: From Protein Sequence to Function, S. Pennington (Editor), M. Dunn (Editor), 2000, Springer Verlag</li>
<li>Proteome Research: Two-Dimensional Gel Electrophoresis and Detection Methods (Principles and Practice), T. Rabilloud (Editor), 2000, Springer Verlag</li>
<li>Proteome and Protein Analysis, R. M. Kamp, D. Kyriakidis, th Choli-Papadopoulou (Editor), 1999, Springer Verlag</li>
<li>Proteome Research: New Frontiers in Functional Genomics, M. R. Wilkins, et al. (Editors), 1997, Springer Verlag</li>
</ul><p>Protein Structure</p><ul>
<li>Structural Bioinformatics, Philip E. Bourne, Helge Weissig (Editors), 2003, John Wiley &amp; Sons</li>
<li>Protein Structure Prediction: Bioinfomatic Approach, I.F. Tsigelny, 2002, International University Line</li>
<li>Introduction to Protein Architecture: The Structural Biology of Proteins, Arthur M. Lesk, 2001, Oxford University Press</li>
<li>Protein Structure Prediction: Methods and Protocols, David M. Webster (Editor), 2000, Humana Press</li>
<li>Introduction to Protein Structure, Carl-Ivar Branden, John Tooze, 1999, Garland Publishing</li>
<li>Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding, Alan Fersht, 1999, Freeman</li>
</ul><p>Pharmacogenomics</p><ul>
<li>Pharmacogenomics: Social, Ethical, and Clinical Dimensions, Mark A. Rothstein (Editor), 2003, Wiley-Liss</li>
<li>Pharmacogenomics: The Search for Individualized Therapies, Julio Licinio, Ma-Li Wong (Editors), 2002, John Wiley &amp; Sons</li>
<li>Pharmacogenomics, Werner Kalow, Urs A. Meyer, Rachel Tyndale (Editors), 2001, Marcel Dekker</li>
<li>Pharmacogenetics and Pharmcogenomics: Recent Conceptual and Technical Advances (Pharmacology, Volume 61, Number 3, 2000), Elliot S. Vesell (Editor), 2000, S. Karger Publishing</li>
<li>Pharmacogenetics, Wendell Weber, 1997, Oxford University Press</li>
</ul><p>DNA Microarrays</p><ul>
<li>Statistical Analysis of Gene Expression Microarray Data, T. P. Speed (Editor), 2003, CRC Press</li>
<li>Microarray Gene Expression Data Analysis: A Beginner's Guide, Helen C. Causton, John Quackenbush, Alvis Brazma, 2003, Blackwell Publishers</li>
<li>The Analysis of Gene Expression Data (Statistics for Biology and Health), G. Parmigiani, E. S. Garrett, R. A. Irizarry, S. Zeger , Graeme Clark (Editors), 2003, Springer Verlag</li>
<li>A Practical Approach to Microarray Data Analysis, Daniel P. Berrar, Werner Dubitzky, Martin Granzow (Editors), 2002, Kluwer Academic Publishers</li>
<li>DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling, Pierre Baldi, G. Wesley Hatfield, 2002, Cambridge University Press</li>
<li>DNA Microarrays: A Molecular Cloning Manual, David Bowtell, Joseph Sambrook (Editors), 2002, Cold Spring Harbor Laboratory</li>
<li>DNA Array Image Analysis: Nuts &amp; Bolts, Gerda Kamberova, Shishir Shah, 2002, DNA Press</li>
<li>Microarray Analysis, Mark Schena, 2002, John Wiley &amp; Sons</li>
<li>A Biologist's Guide to Analysis of DNA Microarray Data, Steen Knudsen, 2002, John Wiley &amp; Sons</li>
<li>Microarrays for an Integrative Genomics (Computational Molecular Biology), Isaac S. Kohane, Alvin Kho, Atul J. Butte, 2002, MIT Press</li>
<li>Microarrays for the Neurosciences: An Essential Guide (Cellular and Molecular Neuroscience), Daniel H. Geschwind, Jeffrey P. Gregg (Editors), 2002, MIT Press</li>
<li>DNA Microarrays: Gene Expression Applications, Bertrand Jordan (Editor), 2001, Springer Verlag</li>
<li>DNA Arrays: Methods and Protocols (Methods in Molecular Biology, Volume 170), Jang B. Rampal (Editor), 2001, Humana Press</li>
<li>DNA Arrays: Technologies and Experimental Strategies, Elena V. Grigorenko (Editor), 2001, CRC Press</li>
<li>Microarray Biochip Technology, Mark Schena (Editor), 2000, Eaton Pub</li>
<li>Expression Genetics: Accelerated and High-Throughput Methods (Biotechniques Update Series), Michael McClelland (Editor), Arthur B. Pardee (Editor), 1999, Eaton Pub</li>
<li>DNA Microarrays: A Practical Approach (Practical Approach Series 205), Mark Schena (Editor), 1999, Oxford Univ Press</li>
<li>cDNA Preparation and Characterization (Methods in Enzymology Volume 303), S.M. Weissman (Editor), 1999, Academic Press</li>
</ul><p>Systems Biology, Genetic and Biochemical Network</p><ul>
<li>Handbook of Graphs and Networks : From the Genome to the Internet, Stefan Bornholdt, Heinz Georg Schuster (Editors), 2003, Vch Verlagsgesellschaft Mbh</li>
<li>Computational Cell Biology, Christopher Fall, Eric Marland, John Wagner, John Tyson (Editors), 2002, Springer Verlag</li>
<li>Gene Regulation and Metabolism: Post-Genomic Computational Approaches (Computational Molecular Biology), Julio Collado-Vides, Ralf Hofestadt (Editors), 2002, MIT Press</li>
<li>Foundations of Systems Biology, Hiroaki Kitano (Editor), 2001, MIT Press</li>
<li>Genomic Regulatory Systems: Development and Evolution, Eric H. Davidson , 2001, Academic Press</li>
<li>Genes &amp; Signals, Mark Ptashne, Alexander Gann, 2001, Cold Spring Harbor Laboratory</li>
<li>Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology), James M. Bower and Hamid Bolouri (Editors), 2001, MIT Press</li>
<li>Protein-Protein Interactions: A Molecular Cloning Manual, Erica Golemis (Editor), 2001, Cold Spring Harbor Laboratory</li>
<li>Computational Analysis of Biochemical Systems: A Practical Guide for Biochemists and Molecular Biologists, Eberhard O. Voit, 2000, Cambridge University Press</li>
<li>Mathematical Physiology, James P. Keener, James Sneyd, 1998, Springer Verlag</li>
</ul><p>&nbsp;</p><p>DNA Sequencing</p><ul>
<li>DNA Sequencing: From Experimental Methods to Bioinformatics (Introduction to Biotechniques Series), Luke Alphey, 1997, Springer Verlag</li>
<li>Automated DNA sequencing and analysis, Adams M.D., Fields C., Venter J.C. (Editors), 1994, Academic Press</li>
</ul><p>&nbsp;</p><p>Apart from above mentioned books, you can also find some useful books links at following mentioned URLs:</p><p>&nbsp;</p><p><a href="http://www.amazon.com/Biological-Sequence-Analysis-Probabilistic-Proteins/dp/0521629713">http://www.amazon.com/Biological-Sequence-Analysis-Probabilistic-Proteins/dp/0521629713</a></p><p><a href="http://www.amazon.com/Bioinformatics-Genes-Proteins-Computers-Advanced/dp/1859960545">http://www.amazon.com/Bioinformatics-Genes-Proteins-Computers-Advanced/dp/1859960545</a></p><p><a href="http://www.amazon.com/Introduction-Bioinformatics-Algorithms-Computational-Molecular/dp/0262101068">http://www.amazon.com/Introduction-Bioinformatics-Algorithms-Computational-Molecular/dp/0262101068</a></p><p><a href="http://books.google.no/books?id=pxSM7R1sdeQC&amp;dq=Pierre+baldi+%2B+bioinformatics&amp;printsec=frontcover&amp;source=bn&amp;hl=en&amp;ei=IoGRS6uCIJT-NYLA8Z0N&amp;sa=X&amp;oi=book_result&amp;ct=result&amp;redir_esc=y#v=onepage&amp;q&amp;f=false">http://books.google.no/books?id=pxSM7R1sdeQC&amp;dq=Pierre+baldi+%2B+bioinformatics&amp;printsec=frontcover&amp;source=bn&amp;hl=en&amp;ei=IoGRS6uCIJT-NYLA8Z0N&amp;sa=X&amp;oi=book_result&amp;ct=result&amp;redir_esc=y#v=onepage&amp;q&amp;f=false</a></p><p><a href="http://www.amazon.com/Statistical-Methods-Bioinformatics-Introduction-Statistics/dp/0387400826">http://www.amazon.com/Statistical-Methods-Bioinformatics-Introduction-Statistics/dp/0387400826</a></p><p>&nbsp;</p><p>If you think your favourite books are not listed then please write it down in comment section for the benefits of other users.&nbsp;Feel free to add many more books in comment section.&nbsp;</p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/39606/amity-university-bioinformatics-summer-program-kolkata</guid>
	<pubDate>Tue, 11 Jun 2019 21:27:10 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/39606/amity-university-bioinformatics-summer-program-kolkata</link>
	<title><![CDATA[Amity University Bioinformatics Summer Program - Kolkata]]></title>
	<description><![CDATA[<p>Registrations are now open for the 2019 Summer Bioinformatics Training program at Amity University, Kolkata. The program will focus on introductory topics for life science students. We will review important history, topics and challenges bioinformatics can help address in the context of basic research, discovery and industry.</p><p>Read more: https://edu.t-bio.info/amity-university-summer-bioinformatics-program-registrations-are-open/</p>]]></description>
	<dc:creator>eliabrodsky</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/11399/next-generation-sequencing-in-r-or-bioconductor-environment</guid>
	<pubDate>Mon, 02 Jun 2014 18:03:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/11399/next-generation-sequencing-in-r-or-bioconductor-environment</link>
	<title><![CDATA[Next generation sequencing in R or bioconductor environment]]></title>
	<description><![CDATA[<p>There are many R software and bioconductor packages for NGS data analysis, some of them are as follows</p><h3><a name="TOC-Biostrings" id="TOC-Biostrings"></a>Biostrings</h3><p>The Biostrings package from Bioconductor provides an advanced environment for efficient sequence management and analysis in R. It contains many speed and memory effective string containers, string matching algorithms, and other utilities, for fast manipulation of large sets of biological sequences. The objects and functions provided by Biostrings form the basis for many other sequence analysis packages. <a href="http://bioconductor.org/packages/release/bioc/html/Biostrings.html">Documentation</a></p><div><div style="text-align: left;"><div style="color: #000000;"><h4><a name="TOC-IRanges-Overview" id="TOC-IRanges-Overview"></a>IRanges Overview</h4><p>IRanges provides the low-level infrastructure and containers for handling sets of integer ranges within Bioconductor's BioC-Seq domain. Its classes and methods provide support for many more high-level packages like GenomicRanges, ShortRead, Rsamtools, etc. <a href="http://bioconductor.org/packages/release/bioc/html/IRanges.html">Documentation</a></p><div style="text-align: right;"><div style="text-align: left;"><h4><a name="TOC-GenomicRanges-Overview" id="TOC-GenomicRanges-Overview"></a>GenomicRanges Overview</h4><p>The <em>GenomicRanges</em> package serves as the foundation for representing genomic locations within the Bioconductor project. It is built upon the <em>IRanges</em> infrastructure and defines three major data containers - <em>GRanges, GRangesList</em> and <em>GappedAlignments</em> - which are supporting other important BioC-Seq packages including <em>ShortRead, Rsamtools, rtracklayer, GenomicFeatures</em> and <em>BSgenome</em>.&nbsp; Compared to the IRanges container, the GRanges/<em>GRangesList</em> classes are more flexible and extensible to store additional information about sequence ranges, such as chromosome identifiers (sequence space), strand information and annotation data. <a href="http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html">Documentation</a></p></div></div></div></div><h3><a name="TOC-Motif-Discovery" id="TOC-Motif-Discovery"></a>Motif Discovery</h3><h4><a name="TOC-cosmo" id="TOC-cosmo"></a>cosmo</h4><p>The cosmo package allows to search a set of unaligned DNA sequences for a shared motif that may function as transcription factor binding site. The algorithm extends the popular motif discovery tool MEME (Bailey and Elkan, 1995) in that it allows the search to be supervised by specifying a set of constraints that the motif to be discovered must satisfy. <a href="http://bioconductor.org/packages/release/bioc/html/cosmo.html">Documentation</a></p></div><div>
<p><span></span><span></span></p>
<div style="color: #0000ff;"><h4><a name="TOC-BCRANK" id="TOC-BCRANK"></a>BCRANK</h4><p>BCRANK is a method that takes a ranked list of genomic regions as input and outputs short DNA sequences that are overrepresented in some part of the list. The algorithm was developed for detecting transcription factor (TF) binding sites in a large number of enriched regions from high-throughput ChIP-chip or ChIP-seq experiments, but it can be applied to any ranked list of DNA sequences. Documentation</p>
<p><a href="http://bioconductor.org/packages/release/bioc/html/BCRANK.html"></a></p>
<p>rGADEM: <a href="http://bioconductor.org/packages/devel/bioc/html/rGADEM.html">Documentation</a></p><p>MotIV: <a href="http://bioconductor.org/packages/devel/bioc/html/MotIV.html">Documentation</a></p></div><h3><a name="TOC-ShortRead" id="TOC-ShortRead"></a>ShortRead</h3><p>The ShortRead package provides input, quality control, filtering, parsing, and manipulation functionality for short read sequences produced by high throughput sequencing technologies. While support is provided for many sequencing technologies, this package is primairly focused on Solexa/Illumina reads. <a href="http://bioconductor.org/packages/release/bioc/html/ShortRead.html">Documentation</a></p><h3><a name="TOC-Rsamtools" id="TOC-Rsamtools"></a>Rsamtools</h3><p>Rsamtools provides functions for parsing and inspecting samtools BAM formatted binary alignment data. SAM/BAM is quickly becoming a universal standard alignment format, and is now supported by a wide variety of alignment tools. <a href="http://bioconductor.org/help/bioc-views/2.7/bioc/html/Rsamtools.html">Documentation</a></p>
<p><a href="http://samtools.sourceforge.net/">Samtools Website</a><br /> <a href="http://bio-bwa.sourceforge.net/">BWA (Burrows-Wheeler Alignment) Website</a><br /><span style="color: #0000ff;"></span></p>
<div style="color: #000000;">&nbsp;</div></div><div>
<p><span style="color: #000000;">Additional tools for SNP analysis:&nbsp;</span></p>
<p><a href="http://bioconductor.org/help/bioc-views/release/bioc/html/snpMatrix.html">snpMatrix</a></p><h3><a name="TOC-BSgenome" id="TOC-BSgenome"></a>BSgenome</h3><p>BSgenome provides an object oriented infrastructure for interacting with a Biostring based genome sequence. BSgenome packages exist for many common genomes, and can be created to represent custom genomes. See the "How to forge a BSgenome data package" Vignette for instructions to create a new BSgenome package if a prebuilt package does not exist for your organism. <a href="http://bioconductor.org/packages/release/bioc/html/BSgenome.html">Documentation</a></p><h3><a name="TOC-rtracklayer" id="TOC-rtracklayer"></a>rtracklayer</h3><p>rtracklayer provides an interface for exporting annotation feature data to various genome browsers and file formats (such as GFF). See the Small RNA Profiling exercise for an example of using rtracklayer to visualize alignment coverage. <a href="http://bioconductor.org/packages/release/bioc/html/rtracklayer.html">Documentation</a></p><h3><a name="TOC-biomaRt" id="TOC-biomaRt"></a>biomaRt</h3><p>The biomaRt package, provides an interface to a growing collection of databases implementing the BioMart software suite (http:// www.biomart.org). The package enables online retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas. This data is retrieved automatically via the Internet, so it's recommended that you cache the data locally, or check versions if your code will be adversely affected by updates to these data. <a href="http://bioconductor.org/packages/release/bioc/html/biomaRt.html">Documentation</a></p><h3><a name="TOC-ChIP-Seq-Analysis-Packages" id="TOC-ChIP-Seq-Analysis-Packages"></a>ChIP-Seq Analysis Packages</h3><p>Bioconductor provides various packages for analyzing and visualizing ChIP-Seq data. Only a small selection of these packages is introduced here. Additional useful introductions to this topic are: <a href="http://www.bioconductor.org/workshops/2009/SeattleJan09/ChIP-seq/">BioC ChIP-seq Case Study</a> and BioC <a href="http://www.bioconductor.org/help/course-materials/2009/SeattleNov09/ChIP-seq/">ChIP-Seq</a>.</p><h4><a name="TOC-chipseq" id="TOC-chipseq"></a>chipseq</h4><p>The chipseq package combines a variety of HT-Seq packages to a pipeline for ChIP-Seq data analysis. <a href="http://bioconductor.org/packages/release/bioc/html/chipseq.html">Documentation</a></p><h4><a name="TOC-BayesPeak" id="TOC-BayesPeak"></a>BayesPeak</h4><p>BayesPeak is a peak calling package for identifying DNA binding sites of proteins in ChIP-Seq experiments. Its algorithm uses hidden Markov models (HMM) and Bayesian statistical methods. The following sample code introduces the identification of peaks with the BayesPeak package as well as the incorporation of read coverage information obtained by the chipseq package. <a href="http://bioconductor.org/packages/release/bioc/html/BayesPeak.html">Documentation</a> [ <a href="http://www.biomedcentral.com/1471-2105/10/299">Publication</a> ]</p><h4><a name="TOC-PICS" id="TOC-PICS"></a>PICS</h4><p>The PICS package applies probabilistic inference to aligned-read ChIP-Seq data in order to identify regions bound by transcription factors. PICS identifies enriched regions by modeling local concentrations of directional reads, and uses DNA fragment length prior information to discriminate closely adjacent binding events via a Bayesian hierarchical t-mixture model. The following sample code uses the test data set from the above BayesPeak package in order to compare the results from both methods by identifying their consensus peak set. <a href="http://www.bioconductor.org/packages/release/bioc/html/PICS.html">Documentation</a> [ <a href="http://www.hubmed.org/display.cgi?uids=20528864">Publication</a> ]</p><h4><a name="TOC-ChIPpeakAnno" id="TOC-ChIPpeakAnno"></a>ChIPpeakAnno</h4><p>The ChIPpeakAnno package provides. batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. It includes functions to retrieve the sequences around peaks, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. The package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages. <a href="http://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html">Documentation</a></p><h4><a name="TOC-Additional-ChIP-Seq-Packages" id="TOC-Additional-ChIP-Seq-Packages"></a>Additional ChIP-Seq Packages</h4><p>DiffBind: <a href="http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html">Documentation</a></p><p>MOSAICS: <a href="http://bioconductor.org/packages/devel/bioc/html/mosaics.html">Documentation</a></p><p>iSeq: <a href="http://bioconductor.org/packages/release/bioc/html/iSeq.html">Documentation</a></p><p>ChIPseqR: <a href="http://bioconductor.org/packages/release/bioc/html/ChIPseqR.html">Documentation</a></p><p>ChiPsim: <a href="http://bioconductor.org/packages/release/bioc/html/ChIPsim.html">Documentation</a></p><p>CSAR: <a href="http://www.bioconductor.org/packages/devel/bioc/html/CSAR.html">Documentation</a></p><p>ChIP-Seq Pipeline: <a href="http://www.bioconductor.org/packages/release/bioc/html/PICS.html">PICS</a>, rGADEM and MotIV (<a href="http://www.rglab.org/pics-and-bioconductor/">developer web site</a>)</p><p>SPP: <a href="http://compbio.med.harvard.edu/Supplements/ChIP-seq/">ChIP-seq processing pipeline</a></p><p><a href="http://compbio.med.harvard.edu/Supplements/ChIP-seq/tutorial.html">SPP Tutorial</a></p><p><a href="http://liulab.dfci.harvard.edu/MACS/index.html">MACS</a></p><p><a href="http://gmdd.shgmo.org/Computational-Biology/ChIP-Seq/download/SIPeS">SIPeS</a></p><h3><a name="TOC-RNA-Seq-Analysis" id="TOC-RNA-Seq-Analysis"></a>RNA-Seq Analysis</h3><h4><a name="TOC-Counting-Reads-that-Overlap-with-Annotation-Ranges-" id="TOC-Counting-Reads-that-Overlap-with-Annotation-Ranges-"></a>Counting Reads that Overlap with Annotation Ranges&nbsp;</h4><p>The GenomicRanges package provides support for importing into R short read alignment data in BAM format (via Rsamtools) and associating them with genomic feature ranges, such as exons or genes. This way one can quantify the number of reads aligning to annotated genomic regions. The package defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome. The two main functions for read counting provided by this infrastructure are <span>countOverlaps <span style="color: #000000;"><span>and</span></span> summarizeOverlaps</span>. For their proper usage, it is important to read the corresponding <a href="http://www.bioconductor.org/packages/devel/bioc/vignettes/GenomicRanges/inst/doc/summarizeOverlaps.pdf">PDF manual</a>. <a href="http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html">Documentation</a></p><h4><a name="TOC-Differential-Gene-Expression-Analysis-with-DESeq" id="TOC-Differential-Gene-Expression-Analysis-with-DESeq"></a>Differential Gene Expression Analysis with DESeq</h4><p>The DESeq package contains functions to call differentially expressed genes (DEGs) in count tables based on a model using the negative binomial distribution. It expects as input a data frame with the raw read counts per region/gene of interest (rows) for each test sample (columns).&nbsp; Such a count table can be imported into R or generated from BAM alignment files using the <span>countOverlaps</span> function as introduced above. <a href="http://www.bioconductor.org/packages/release/bioc/html/DESeq.html">Documentation</a></p><h4><a name="TOC-Differential-Gene-Expression-Analysis-with-edgeR" id="TOC-Differential-Gene-Expression-Analysis-with-edgeR"></a>Differential Gene Expression Analysis with edgeR</h4><p>The edgeR package uses empirical Bayes estimation and exact tests based on the negative binomial distribution to call differentially expressed genes (DEGs) in count data.&nbsp;</p>
<p><a href="http://www.bioconductor.org/packages/release/bioc/html/edgeR.html">Documentation</a></p>
<p><span style="color: #000000;">A variety of additional R packages are available for normalizing RNA-Seq read count data and identifying differentially expressed genes (DEG): <br /> </span></p><p><a href="http://bioconductor.org/packages/devel/bioc/html/easyRNASeq.html">easyRNASeq</a> (simplifies read counting per genome feature)</p><p><a href="http://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html">DEXSeq</a> (Inference of differential exon usage);&nbsp;<a href="http://www.bioconductor.org/packages/release/data/experiment/html/parathyroidSE.html">parathyroidSE</a> explains how to generate exon read counts in R</p><p><a href="http://bioconductor.org/packages/release/bioc/html/DEGseq.html">DEGseq</a></p><p><a href="http://www.bioconductor.org/packages/release/bioc/html/baySeq.html">baySeq</a> (also see: <a href="http://www.bioconductor.org/packages/release/bioc/html/segmentSeq.html">segmentSeq</a>)</p><p><a href="http://bioconductor.org/packages/release/bioc/html/Genominator.html">Genominator</a> (<a href="http://www.hubmed.org/display.cgi?uids=20167110">Bullard et al. 2010</a>)</p><div style="text-align: right;"><div style="text-align: left;"><h4><a name="TOC-Detection-of-Alternative-Splice-Junctions" id="TOC-Detection-of-Alternative-Splice-Junctions"></a>Detection of Alternative Splice Junctions</h4>
<p><span style="color: #000000;">Another utility of RNA-Seq experiments is the analysis of splice junctions. The following software suggestions provide this utility:</span></p>
<p><a href="http://woldlab.caltech.edu/rnaseq/">ERANGE<br /> </a><a href="http://tophat.cbcb.umd.edu/">TopHat</a></p><p><a href="http://biogibbs.stanford.edu/%7Ekinfai/SpliceMap/">SpliceMap</a></p><p><a href="http://solidsoftwaretools.com/gf/project/splitseek/">SplitSeek</a></p><h3><a name="TOC-DNA-Methylation-Data-Analysis" id="TOC-DNA-Methylation-Data-Analysis"></a>DNA-Methylation Data Analysis</h3><div><ul>
<li><span style="font-size: 10pt;"><a href="http://www.bioconductor.org/help/course-materials/2012/BiocEurope2012/mattia_pelizzola_methylPipe.pdf">methylPipe</a></span></li>
<li><span style="font-size: 10pt;"><a href="http://www.bioconductor.org/packages/devel/bioc/html/bsseq.html">bsseq</a></span></li>
<li><a href="http://www.bioconductor.org/packages/devel/bioc/html/BiSeq.html">BiSeq</a></li>
<li>Much more under <a href="http://www.bioconductor.org/packages/devel/BiocViews.html#___DNAMethylation">BiocViews</a></li>
</ul></div></div></div><h3><a name="TOC-HT-Seq-Data-Visualization" id="TOC-HT-Seq-Data-Visualization"></a>HT-Seq Data Visualization</h3>
<p><a href="http://www.bioconductor.org/packages/release/bioc/html/ggbio.html">ggbio</a>: ggplot2 extension for genomics data (<a href="http://tengfei.github.com/ggbio/">online manual</a>) <a href="http://www.bioconductor.org/packages/devel/bioc/html/Gviz.html">Gviz</a>:&nbsp;Plotting data and annotation information along genomic coordinates <a href="http://bioconductor.org/packages/release/bioc/html/HilbertVis.html">HilbertVis</a>: Hilbert genome plots</p>
<p><a href="http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html">GenomeGraphs</a>: Plotting genomic information from Ensembl</p><p><a href="http://www.hubmed.org/display.cgi?uids=18507856">TileQC</a>: Flow Cell Quality Visualization</p><p><a href="http://bioconductor.org/packages/release/bioc/html/rtracklayer.html">rtracklayer</a>: R interface to genome browsers</p><p><a href="http://genoplotr.r-forge.r-project.org/">genoPlotR</a>: Plotting maps of genes and genomes</p><p><a href="http://bioconductor.org/packages/release/bioc/html/Genominator.html">Genominator</a>: Tools for storing, accessing, analyzing and visualizing genomic data.</p><p>&nbsp;</p><p>To install all packages</p><blockquote><p>source("http://bioconductor.org/biocLite.R")<br />biocLite()<br />biocLite(c("ShortRead", "Biostrings", "IRanges", "BSgenome", "rtracklayer", "biomaRt", "chipseq", "ChIPpeakAnno", "Rsamtools", "BayesPeak", "PICS", "GenomicRanges", "DESeq", "edgeR", "leeBamViews", "GenomicFeatures", "BSgenome.Celegans.UCSC.ce2"))</p></blockquote></div>]]></description>
	<dc:creator>John Parker</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/19820/rstudio</guid>
	<pubDate>Sat, 27 Dec 2014 06:50:58 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/19820/rstudio</link>
	<title><![CDATA[RStudio]]></title>
	<description><![CDATA[<p>RStudio IDE is a powerful and productive user interface for R. It&rsquo;s free and open source, and works great on Windows, Mac, and Linux.</p>
<p>The developers and expert trainers are the authors of several popular R packages, including ggplot2, plyr, lubridate, and others.</p>
<p>More at http://www.rstudio.com/</p>
<p>http://www.rstudio.com/products/RStudio/</p><p>Address of the bookmark: <a href="http://www.rstudio.com/" rel="nofollow">http://www.rstudio.com/</a></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/21312/r-for-microsoft-excel</guid>
	<pubDate>Wed, 18 Feb 2015 00:43:27 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/21312/r-for-microsoft-excel</link>
	<title><![CDATA[R for Microsoft Excel]]></title>
	<description><![CDATA[<div><p>If you currently use a spreadsheet like Microsoft Excel for data analysis, you might be interested in taking a look at this <a href="https://districtdatalabs.silvrback.com/intro-to-r-for-microsoft-excel-users" target="_blank">tutorial on how to transition from Excel to R</a>&nbsp;by Tony Ojeda. The tutorial explains how to use R functions in place of Excel formulas, including tools like =AVERAGE and =VLOOKUP. For the most part, it uses modern R packages to keep the R code clear and concise.</p><p>You'll likely still be using Excel as a data source, though, so you'll also want to check out this <a href="http://www.milanor.net/blog/?p=779" target="_blank">guide to importing data from Excel to R</a> from MilanoR.</p></div><p>Reference http://www.r-bloggers.com/an-r-tutorial-for-microsoft-excel-users/</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>

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