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adamsardar / metaDEGth

metaDEGth: meta-analysis of Differentially Expressed Genes using parametric, empirically-derived P-value distributions
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Incorporate validation data: GSE100118 #1

Open adamsardar opened 6 years ago

adamsardar commented 6 years ago

Uncovering mechanisms of early human lineage specification by CRISPR/Cas9-mediated genome editing

The authors knock down the pluripotent TF OCT4 by CRISPR and collect RNAseq measurements (aka peturb-Seq ),

This will be a useful 'gold-standard' validation set

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100118

adamsardar commented 4 years ago

After playing with this dataset a little, the pre-packaged RPKM values are not sufficient. Will need to download the raw reads and psuedo-align with kallisto.

Good discussion here: https://support.bioconductor.org/p/73289/

adamsardar commented 4 years ago

I don't think that I have processed the data correctly - this is a single cell RNAseq experiment.

https://www.kallistobus.tools/tutorials

Time to study and learn.