# 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

[^Costa-Silva_2017]: Costa-Silva J, Domingues D, Lopes FM. RNA-Seq differential expression analysis: An extended review and a software tool. PLoS One. 2017 Dec 21;12(12):e0190152. doi: 10.1371/journal.pone.0190152. PMID: 29267363; PMCID: PMC5739479.

[^McDermaid_2019]: McDermaid A, Monier B, Zhao J, Liu B, Ma Q. Interpretation of differential gene expression results of RNA-seq data: review and integration. Brief Bioinform. 2019 Nov 27;20(6):2044-2054. doi: 10.1093/bib/bby067. PMID: 30099484; PMCID: PMC6954399.

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.