<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/27225?offset=80 https://bioinformaticsonline.com/opportunity/view/43272/bioinformatics-head-bioinformatics-manager-iii-cancer-genomics-research-laboratory-at-frederick-national-laboratory Wed, 18 Aug 2021 00:19:48 -0500 <![CDATA[Bioinformatics Head (Bioinformatics Manager III), Cancer Genomics Research Laboratory at Frederick National Laboratory]]> Frederick National Laboratory seeking an enthusiastic, creative, and seasoned bioinformatics professional to join our leadership team and direct the exceptional Bioinformatics Group at the Cancer Genomics Research Laboratory (CGR). CGR has a diverse team of bioinformatics and computational scientists that support all areas of bioinformatics and data analysis (infrastructure, data QC, pipeline development and maintenance, data curation and sharing, methodology development, statistical analyses, machine learning approaches, and scientific interpretation).

More at https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leidosbiomed&id=2040

]]> https://bioinformaticsonline.com/blog/view/42974/list-of-bioinformatics-packages-for-ngs-analysis Sat, 20 Mar 2021 00:28:51 -0500 https://bioinformaticsonline.com/blog/view/42974/list-of-bioinformatics-packages-for-ngs-analysis <![CDATA[List of bioinformatics packages for NGS analysis !]]> Package suites gather software packages and installation tools for specific languages or platforms. We have some for bioinformatics software.

  • Bioconductor – A plethora of tools for analysis and comprehension of high-throughput genomic data, including 1500+ software packages. [ paper-2004 | web ]
  • Biopython – Freely available tools for biological computing in Python, with included cookbook, packaging and thorough documentation. Part of the Open Bioinformatics Foundation. Contains the very useful Entrez package for API access to the NCBI databases. [ paper-2009 | web ]
  • Bioconda – A channel for the conda package manager specializing in bioinformatics software. Includes a repository with 3000+ ready-to-install (with conda install) bioinformatics packages. [ paper-2018 | web ]
  • BioJulia – Bioinformatics and computational biology infastructure for the Julia programming language. [ web ]
  • Rust-Bio – Rust implementations of algorithms and data structures useful for bioinformatics. [ paper-2016 ]
  • SeqAn – The modern C++ library for sequence analysis.
]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/38819/upsetr-an-r-package-for-the-visualization-of-intersecting-sets-and-their-properties Mon, 28 Jan 2019 18:38:44 -0600 https://bioinformaticsonline.com/bookmarks/view/38819/upsetr-an-r-package-for-the-visualization-of-intersecting-sets-and-their-properties <![CDATA[UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties]]> UpSetR generates static UpSet plots. 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.

For further details about the original technique see the UpSet website. You can also check out the UpSetR shiny app. Here is the source code for the shiny wrapper.

A Python package called py-upset to create UpSet plots has been created by GitHub user ImSoErgodic.

Address of the bookmark: https://github.com/hms-dbmi/UpSetR/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/44487/r-package-for-pca-analysis Sun, 24 Mar 2024 20:06:24 -0500 https://bioinformaticsonline.com/bookmarks/view/44487/r-package-for-pca-analysis <![CDATA[R Package for PCA Analysis]]> An R package for performing principal component analysis (PCA) of genomics data. The package performs PCA, generates the publication-ready plots, and identifies population-specific outlier individuals. The package can be accessed on GitHub: https://github.com/Devashish13/PopulationStructure

Address of the bookmark: https://rpubs.com/Devashish13/PCAGenomics

]]> LEGE https://bioinformaticsonline.com/blog/view/37049/chromomap-an-r-package-for-interactive-visualization-and-mapping-of-human-chromosomes Mon, 25 Jun 2018 17:22:24 -0500 https://bioinformaticsonline.com/blog/view/37049/chromomap-an-r-package-for-interactive-visualization-and-mapping-of-human-chromosomes <![CDATA[chromoMap-An R package for Interactive visualization and mapping of human chromosomes]]> chromoMap is an R package that provides interactive, configurable and elegant graphics visualization of the human chromosomes allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces a special plot viz. the "chromosome heatmap" that, in addition to mapping elements, can visualize the data associated with chromosome elements (like gene expression) in the form of heat colors which can be highly advantageous in the scientific interpretations and research work. Because of the enormous size of the chromosomes, it is impractical to visualize each element on the same plot. But chromoMap plots provide a magnified view for each of chromosome location to render additional information and visualization specific for that location. You can map thousands of genes and can view all mappings easily. Users can investigate the detailed information about the mappings (like gene names or total genes mapped on a location) or can view the magnified single or double stranded view of the chromosome at a location showing each mapped element in sequential order (You will see in the demos below). Not ony that, the plots can be saved as HTML documents that can be customized and shared easily. In addition, you can include them in R Markdown or in R Shiny applications.

https://cran.r-project.org/web/packages/chromoMap/index.html

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/38541/geneoverlap-an-r-package-to-test-and-visualize-gene-overlaps Thu, 27 Dec 2018 19:45:52 -0600 https://bioinformaticsonline.com/bookmarks/view/38541/geneoverlap-an-r-package-to-test-and-visualize-gene-overlaps <![CDATA[GeneOverlap: An R package to test and visualize gene overlaps]]> Overlapping gene lists can reveal biological meanings and may lead to novel hypotheses. For example, histone modification is an important cellular mechanism that can pack and re-pack chromatin. By making the chromatin structure more dense or loose, the gene expression can be turned on or off. Tri-methylation on lysine 4 of histone H3 (H3K4me3) is associated with gene activation and its genome-wide enrichment can be mapped by using ChIP-seq experiments. Because of its activating role, if we overlap the genes that are bound by H3K4me3 with the genes that are highly expressed, we should expect a positive association. Similary, we can perform such kind of overlapping between the gene lists of different histone modifications with that of various expression groups and establish each histone modification’s role in gene regulation.

Address of the bookmark: https://bioconductor.org/packages/release/bioc/vignettes/GeneOverlap/inst/doc/GeneOverlap.pdf

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41362/genemates-an-r-package-for-detecting-horizontal-gene-co-transfer-between-bacteria-using-gene-gene-associations-controlled-for-population-structure Sat, 07 Mar 2020 05:52:20 -0600 https://bioinformaticsonline.com/bookmarks/view/41362/genemates-an-r-package-for-detecting-horizontal-gene-co-transfer-between-bacteria-using-gene-gene-associations-controlled-for-population-structure <![CDATA[GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene Associations Controlled for Population Structure]]> GeneMates is an R package implementing a network approach to identify horizontal gene co-transfer (HGcoT) between bacteria using whole-genome sequencing (WGS) data. It is particularly useful for investigating intra-species HGcoT, where presence-absence status of acquired genes is usually confounded by bacterial population structure due to clonal reproduction.

https://www.biorxiv.org/content/10.1101/2020.02.29.970970v1

Address of the bookmark: https://github.com/wanyuac/GeneMates

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/44414/reconplot-an-r-package-for-the-visualization-and-interpretation-of-genomic-rearrangements Thu, 14 Dec 2023 12:33:19 -0600 https://bioinformaticsonline.com/bookmarks/view/44414/reconplot-an-r-package-for-the-visualization-and-interpretation-of-genomic-rearrangements <![CDATA[ReConPlot: an R package for the visualization and interpretation of genomic rearrangements]]> ReConPlot (REarrangement and COpy Number PLOT), an R package that provides functionalities for the joint visualization of SCNAs and SVs across one or multiple chromosomes. ReConPlot is based on the popular ggplot2 package, thus allowing customization of plots and the generation of publication-quality figures with minimal effort.

Address of the bookmark: https://academic.oup.com/bioinformatics/article/39/12/btad719/7460198?login=false

]]> LEGE https://bioinformaticsonline.com/videolist/watch/14218/pimp-your-brain-bioinformatics Wed, 20 Aug 2014 22:09:21 -0500 https://bioinformaticsonline.com/videolist/watch/14218/pimp-your-brain-bioinformatics <![CDATA[Pimp your brain: Bioinformatics]]> Jan Lisec from the Max Planck Institute of Molecular Plant Physiology explains, in this "pimp your brain" episode, what bioinformatics is and why bioinformatics is so important and indispensable for biological research. In the video serial "Pimp your brain" scientists from the Max Planck Institute of Molecular Plant Physiology describe their research. More videos from the 'Pimp your brain' serial are available on www.youtube.com/playlist?list=PL-l9VItC9Gn2Ur2Xj6PTOAkjLUlVPbIOO More videos are available on www.mpimp-golm.mpg.de]]> https://bioinformaticsonline.com/opportunity/view/22285/project-associate-bioinformatics-iit-mandi Wed, 06 May 2015 06:18:47 -0500 <![CDATA[Project Associate Bioinformatics @ IIT Mandi]]> Eligibility : MSc(Bio-Informatics, Bio-Tech), BSc, BE/B.Tech(Bio-Medical /Bio-Technology Engg, CSE)

Location : Kulu

Job Category : Govt Jobs, Research

Last Date : 20 May 2015

Job Type : Full Time

Hiring Process : Walk - In
IIT Mandi - Job Details
IIT Mandi

Project Associate Bioinformatics Job vacancies in IIT Mandi on purely temporary

Project: “Exploring the Human Microbiome: A hunt for the candidates for Pre- and Pro-biotics.”

Minimum Qualification and Experience: M.Sc. in Bioinformatics OR B.Tech / BE in Bioinformatics OR M. Sc. in Biotechnology / Life sciences or related areas with Diploma or relevant experience in Bioinformatics OR B.Tech in Biotechnology / Computer Science or MCA or B. Sc. in Life Sciences or related areas with PG diploma in Bioinformatics. Candidates with experience in NGS data handling and analysis will be preferred. Tenure: Initially for one year, extendable based upon performance.

No of Posts: 01

Salary: Rs. 12000- 18000/- per month.

How to apply

Interested candidates can come for a Walk-in-Interview on 20th May 2015 starting at 8:30 AM at the Academic Block, Indian Institute of Technology (IIT), Mandi, Vallabh College Campus, Near Bus Stand, Mandi, HP. The candidates should bring along their curriculum vitae (CV) and copies of educational and experience certificates. In case of any queries please contact: Dr. Tulika Prakash Srivastava (Principal Investigator), Indian Institute of Technology Mandi, Near Bus Stand Mandi - 175 001, Himachal Pradesh.

More at

http://www.iitmandi.ac.in/administration/advrt/Walk-in-interview_Ad.pdf

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