Resources.md

0-vii. Resources

1. Recommended Reading and RNA-seq Resources

• Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
• Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
• Key tool papers: HISAT, StringTie, BallGown, HTSeq, EdgeR.
• RNA-seqlopedia (Includes a very comprehensive review of library construction concepts)
• List of RNA-Seq bioinformatics tools
• A survey of best practices for RNA-seq data analysis - 2016
• RNA Sequencing and Analysis - 2015 review
• Comparative analysis of RNA sequencing methods
• RNA-seq Data: Challenges in and Recommendations for Experimental Design and Analysis
• RNA Bioinformatics (a 25 chapter book)
• Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
• Differential analysis of gene regulation at transcript resolution with RNA-seq
• Measurement of mRNA abundance using RNA-seq data:RPKM measure is inconsistent among samples
• Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences
• Methods to study splicing from high-throughput RNA sequencing data
• Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
• A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium (SEQC)
• ENCODE RNA-seq Standards
• The RNA-seq blog - recent developments in RNA-seq technology and analysis
• Proportionality: A Valid Alternative to Correlation for Relative Data
• NCBI Hackathons RNA Mapping Tutorial
• RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR

2. Unix/Linux Tutorials

• A UNIX command cheat sheet
• A UNIX tutorial for beginners
• A UNIX and Perl primer for biologists
• A detailed Biostars thread describing resources for learning Unix
• A codecademy tutorial to Learn the Command Line
• A command-line linux tutorial in your browser

3. Text Editor (Vi/Vim) Tutorials

• An interactive Vim tutorial
• Vim Adventures - a graphical game to help learn Vim
• Vim Graphical Cheat Sheets
• Vi tutorial and advanced features

4. R Tutorials

• An R command cheat sheet
• The official R intro manual
• Rseek, a search engine for R related questions
• A detailed BioStars thread describing resources for learning R
• Data Camp - R Tutorials and Data Analysis Courses
• Swirl - Learn R, in R.
• Quick and Dirty Guide to R
• Basic R Introduction

5. Supplementary Materials Relating to the Hands On Tutorials of this Course

• Description of the ERCC spike-in controls used in the tutorial data
• Description of the Human Brain Reference (HBR) sample used to generate the tutorial data
• Description of the Universal Human Reference (UHR) sample used to generate the tutorial data

6. Resources to help find RNA-seq Data Sets

• GEO: The Gene Expression Omnibus
• GXA: the EBI Expression Atlas]
• SHARQ: Search public, human, RNA-seq experiments by cell, tissue type, and other features

7. General Bioinformatics Resources

• Web Based Interactive Resources To Learn Programming And/Or Bioinformatics
• The Bioinformatics Links Directory
• The periodic table of bioinformatics - A list of popular bioinformatics resources and tools
• A list of Genome Analysis Platforms like Galaxy, BaseSpace, etc.
• BioLinux - An Ubuntu Linux system with many Bioinformatics tools pre-installed
• CloudBioLinux - A cloud ready version of BioLinux

8. Getting More Help

• Biostars - A forum for the bioinformatics community
• SEQanswers - A forum for the next generation sequencing community

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