<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/43863?offset=70 https://bioinformaticsonline.com/pages/view/35805/python-learning-resources-for-bioinformatics-and-computational-biologist Fri, 02 Mar 2018 06:54:15 -0600 https://bioinformaticsonline.com/pages/view/35805/python-learning-resources-for-bioinformatics-and-computational-biologist <![CDATA[Python learning resources for bioinformatics and computational biologist !]]> Python is a general-purpose language, which means it can be used to build just about anything, which will be made easy with the right tools/libraries.

Professionally, Python is great for backend web development, data analysis, artificial intelligence, and scientific computing. Many developers have also used Python to build productivity tools, games, and desktop apps, so there are plenty of resources to help you learn how to do those as well.

For pros and cons visit http://www.bestprogramminglanguagefor.me/why-learn-python and http://bioinformaticsonline.com/discussion/view/459/python-vs-perl

More resources at https://github.com/CodementorIO/Python-Learning-Resources

Following are the list of useful python programming resources:

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43042/bioinformatics-in-thailand Wed, 28 Apr 2021 02:04:56 -0500 https://bioinformaticsonline.com/bookmarks/view/43042/bioinformatics-in-thailand <![CDATA[Bioinformatics in Thailand !]]> Our international PhD and master programs are designed for students who desire focused training in the elements of biology, computer science, and information technology needed for a successful career in the exciting new discipline of Bioinformatics & Systems Biology. Students in our program will receive comprehensive training in omics analysis, database design and management, software engineering and programming (including web-based development), simulation techniques and modeling, and data integration. Each student will apply their skills to a practical project, where they will design and implement a solution to a real-world problem under the guidance of an experienced mentor in industry or academia.

https://bioinformatics.kmutt.ac.th/about.html

Duangrudee Tanramluk (Ajarn Wi) uses computational biology and machine learning to tackle the key to drug design problems via MANORAA webserver.

https://mb.mahidol.ac.th/en/bioinformatics/

https://graduate.mahidol.ac.th/inter/

This international Doctorate programme is designed to further broaden students’ knowledge in Bioinformatics and Molecular Biology to their maximum capability. 

http://www.mbb.psu.ac.th/programmes/phd

Ph.D. program in Bioinformatics and Computational Biology is a joint effort of the Faculty of Science and Faculty of Medicine, Chulalongkorn University. The program has study plans for both applicants who hold a bachelor’s degree and applicants who hold a master’s degree in any related fields of study.

http://www.bioinfo.sc.chula.ac.th/ph-d-program-specialization/

Additional detail 

https://www.biotec.or.th/en/index.php/research/research-units/genome-technology-research-unit

https://tbrcnetwork.org/labtbrc/index.php/bioinformatics-and-chemoinformatics/

https://genomicsthailand.com/Genomic/home

Address of the bookmark: https://bioinformatics.kmutt.ac.th/

]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/43552/understanding-pango-networks Sat, 16 Oct 2021 14:02:36 -0500 https://bioinformaticsonline.com/bookmarks/view/43552/understanding-pango-networks <![CDATA[Understanding pango networks !]]> In the vast majority of instances it is expected that Pango lineage names and designations will conform to the following rules. These rules also act as guidelines for the decisions made by the Lineage Designation Committee.

https://www.pango.network/the-pango-nomenclature-system/statement-of-nomenclature-rules/

https://www.pango.network/how-does-the-system-work/what-are-pango-lineages/

Reference paper

https://www.nature.com/articles/s41564-020-0770-5

Address of the bookmark: https://www.pango.network/the-pango-nomenclature-system/statement-of-nomenclature-rules/

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/44601/free-resources-to-learn-statistics Sat, 06 Jul 2024 10:30:50 -0500 https://bioinformaticsonline.com/bookmarks/view/44601/free-resources-to-learn-statistics <![CDATA[Free resources to learn statistics]]> Welcome to the course notes for STAT 414: Introduction to Probability Theory. These notes are designed and developed by Penn State's Department of Statistics and offered as open educational resources. These notes are free to use under Creative Commons license CC BY-NC 4.0.

 

A free online version of the second edition of the book based on Stat 110, Introduction to Probability by Joe Blitzstein and Jessica Hwang, is now available at http://probabilitybook.net

Print copies are available via CRC Press, Amazon, and elsewhere. 

Stat110x is also available as an edX course. Free signup at https://www.edx.org/course/introduction-to-probability-0

The edX course focuses on animations, interactive features, readings, and problem-solving, and is complementary to the Stat 110 lecture videos on YouTube, which are available at https://goo.gl/i7njSb

The Stat110x animations are available within the course and at https://goo.gl/g7pqTo

https://projects.iq.harvard.edu/stat110/home 

Address of the bookmark: https://online.stat.psu.edu/stat414/

]]> BioStar https://bioinformaticsonline.com/pages/view/34465/rnaseq-data-analysis-links Mon, 27 Nov 2017 16:28:11 -0600 https://bioinformaticsonline.com/pages/view/34465/rnaseq-data-analysis-links <![CDATA[RNAseq data analysis links !]]> RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping.

A survey of best practices for RNA-seq data analysis

RNA-seq workflow: gene-level exploratory analysis and DE

RNAseq analysis notes from Tommy Tang

Analysis of RNA ‐ Seq Data

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.

EBI RNA-Seq exercise

An open RNA-Seq data analysis pipeline tutorial with an example

RNA-Seq Analysis Workflow

Transcript-level expression analysis of RNA-seq experiments

]]> Robert M Willioms https://bioinformaticsonline.com/bookmarks/view/38762/katuali-is-a-flexible-consensus-pipeline-implemented-in-snakemake-to-basecall-assemble-and-polish-oxford-nanopore-technologies-sequencing-data Tue, 22 Jan 2019 06:26:55 -0600 https://bioinformaticsonline.com/bookmarks/view/38762/katuali-is-a-flexible-consensus-pipeline-implemented-in-snakemake-to-basecall-assemble-and-polish-oxford-nanopore-technologies-sequencing-data <![CDATA[Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data]]>
  • Run a pipeline processing fast5s to a consensus in a single command.
  • Recommended fixed "standard" and "fast" pipelines.
  • Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath.
  • Seemless distribution of tasks over local or distributed compute.
  • Highly configurable.
  • Open source (Mozilla Public License 2.0).

    • Documentation can be found at https://nanoporetech.github.io/katuali/.

    Address of the bookmark: https://github.com/nanoporetech/katuali

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/39441/snakepipes-a-toolkit-based-on-snakemake-and-python-for-analysis-of-ngs-data Thu, 30 May 2019 04:06:13 -0500 https://bioinformaticsonline.com/bookmarks/view/39441/snakepipes-a-toolkit-based-on-snakemake-and-python-for-analysis-of-ngs-data <![CDATA[snakepipes: A toolkit based on snakemake and python for analysis of NGS data]]> snakePipes are flexible and powerful workflows built using snakemake that simplify the analysis of NGS data.

    • DNA-mapping*
    • ChIP-seq*
    • RNA-seq*
    • ATAC-seq*
    • scRNA-seq
    • Hi-C
    • Whole Genome Bisulfite Seq/WGBS

    (*Also available in "allele-specific" mode)

    snakePipes can be installed via conda :

    'conda install -c mpi-ie -c bioconda -c conda-forge snakePipes'.

    Source code (https://github.com/maxplanck-ie/snakepipes) and documentation (https://snakepipes.readthedocs.io/en/latest/) are available online.

    Address of the bookmark: https://github.com/maxplanck-ie/snakepipes

    ]]>     Jit     https://bioinformaticsonline.com/news/view/2267/added-video-feature-in-bol Tue, 13 Aug 2013 17:42:16 -0500 https://bioinformaticsonline.com/news/view/2267/added-video-feature-in-bol <![CDATA[Added video feature in BOL]]> Just in: Added video features in BOL, now you can watch and share your favourite bioinformatics video tutorials.

    Share your favourite video tutorial or lectures on BOL at http://bioinformaticsonline.com/videolist/all . You can also add video in you groups.

    Note: Other than bioinformatics video material/tutorial will be deleted without any prior warning.

    ]]>     Jitendra Narayan     https://bioinformaticsonline.com/bookmarks/view/3965/ruby-and-bioruby-tutorials Mon, 26 Aug 2013 17:18:28 -0500 https://bioinformaticsonline.com/bookmarks/view/3965/ruby-and-bioruby-tutorials <![CDATA[Ruby and BioRuby Tutorials]]> Collections of Ruby and BioRuby learning materials.

    BioRuby paper link : http://bioinformatics.oxfordjournals.org/content/26/20/2617.abstract

    Address of the bookmark: http://www.codeschool.com/paths/ruby

    ]]>     Jitendra Narayan     https://bioinformaticsonline.com/bookmarks/view/12206/bioinformatics-algorithms-tutorials Tue, 24 Jun 2014 00:10:45 -0500 https://bioinformaticsonline.com/bookmarks/view/12206/bioinformatics-algorithms-tutorials <![CDATA[Bioinformatics algorithms tutorials]]> Useful bioinformatics tutorial, such as

    De Bruijn Graphs for NGS Assembly
    Algorithms for PacBio Reads
    Software and Hardware Concepts for Bioinformatics
    Finding us in Homolog.us (Search Algorithms)
    NGS Genome and RNAseq Assembly - a Hands on Primer
    Introduction to PERL, Python, R and C/C++ for Bioinformatics

    Address of the bookmark: http://www.homolog.us/Tutorials/

    ]]>     John Parker