Incorporate validation data: peturb-seq/CRISPR-seq (GSE90063)

adamsardar / metaDEGth

metaDEGth: meta-analysis of Differentially Expressed Genes using parametric, empirically-derived P-value distributions

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Incorporate validation data: peturb-seq/CRISPR-seq (GSE90063) #11

Open adamsardar opened 5 years ago

adamsardar commented 5 years ago

Much like GSE100118 and GSE74355, the peturb-seq set has a variety of knockdown targets and functional effects. This could make for an excellent validation set.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE90063

See: Dixit A, Parnas O, Li B, Chen J, Fulco CP, Jerby-Arnon L, et al. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Cell. Elsevier; 2016;167: 1853–1866.e17.

adamsardar commented 5 years ago

This looks pretty involved - I need to deconvolve the scRNAseq and all. Move it to a later milestone