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Additional Resources |
## RNA-seq Bioinformatics
Introduction to bioinformatics for RNA sequence analysis
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- RNA sequencing: the teenage years
- 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
- Discussion of Count Normalization Approaches
- 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
- A UNIX command cheat sheet
- A UNIX tutorial for beginners
- A UNIX and Perl primer for biologists
- A command-line bootcamp
- 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
- A tutorial on terminal basics (with web-based sandbox)
- An interactive Vim tutorial
- Vim Adventures - a graphical game to help learn Vim
- Vim Graphical Cheat Sheets
- Vi tutorial and advanced features
- Introduction to R (GenViz.org)
- 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
- 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
- GEO: The Gene Expression Omnibus
- GXA: the EBI Expression Atlas
- SHARQ: Search public, human, RNA-seq experiments by cell, tissue type, and other features
- Web Based Interactive Resources To Learn Programming And/Or Bioinformatics
- 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
- sandbox.io - Interactive bioinformatics tutorials