Giters

latch-verified / diff-exp

Differential expression analysis.

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

Latch Verified

Differential Expression

Latch Verified

Reveal statistically significant genes and transcripts from count matrices.

Current Release License Commit Activity Commits since Last Release

Hosted Interface · SDK Documentation · Slack Community

Using RNA-seq to generate matrices of transcript and gene abundances has become a staple technique for measuring cell state.1 Often it is desirable to use statistical techniques to compare these count matrices across different experimental conditions to reveal genes that change.2

A software benchmark conducted by Costa Silva et. al revealed DESeq2 to be the most performant. For each of a list of tools, reported significant genes were compared against ground-truth genes derived from qRT-PCR, and DESeq2 consistently showed the highest sensitivity (TPR) and accuracy.

table

Footnotes

  1. Stark, Rory; Grzelak, Marta; Hadfield, James (2019). RNA sequencing: the teenage years. Nature Reviews Genetics, (), –. doi:10.1038/s41576-019-0150-2 ↩

  2. Costa-Silva J, Domingues D, Lopes FM (2017) RNA-Seq differential expression analysis: An extended review and a software tool. PLoS ONE 12(12): e0190152. https://doi.org/10.1371/journal.pone.0190152 ↩

About

Differential expression analysis.

Languages

Language:Python 51.5%Language:R 28.4%Language:HTML 14.8%Language:Just 3.4%Language:Dockerfile 1.8%Language:Shell 0.1%