Analysis Resources

Here we provide links to software used to analyze RNA-seq expression matrices.

Resource Collections

  • https://github.com/twbattaglia/RNAseq-workflow

  • https://github.com/jdidion/biotools

Differential Expression Analysis Tools

  • +voom

  • NOIseq 2012

  • DESeq2 2014

  • edgeR 2010

  • baySeq 2010

  • Cuffdiff2 2013

  • DEGseq 2009

  • SAMseq 2013

  • sleuth 2017 https://github.com/pachterlab/sleuth

  • limma 2015

  • consensus methods

Reviews of DGE Methods

  • Contrast creation guide

Alignment Tools

  • …

Single-Cell RNA-Seq

  • scanpy

References

Li WV, Li JJ. Modeling and analysis of RNA-seq data: a review from a statistical perspective. Quant Biol. 2018;6(3):195-209. doi:10.1007/s40484-018-0144-7

Stark R, Grzelak M, Hadfield J. RNA sequencing: the teenage years. Nat Rev Genet. 2019 Nov;20(11):631-656. doi: 10.1038/s41576-019-0150-2. Epub 2019 Jul 24. PMID: 31341269.

Byron SA, Van Keuren-Jensen KR, Engelthaler DM, Carpten JD, Craig DW. Translating RNA sequencing into clinical diagnostics: opportunities and challenges. Nat Rev Genet. 2016 May;17(5):257-71. doi: 10.1038/nrg.2016.10. Epub 2016 Mar 21. PMID: 26996076; PMCID: PMC7097555.

Kakati T, Bhattacharyya DK, Barah P, Kalita JK. Comparison of Methods for Differential Co-expression Analysis for Disease Biomarker Prediction. Comput Biol Med. 2019 Oct;113:103380. doi: 10.1016/j.compbiomed.2019.103380. Epub 2019 Aug 10. PMID: 31415946.