RNA-seq

JR Jeremy Rich
MB Melanie Bennaroch
LN Laura Notel
PP Polina Patalakh
JA Julien Alberola
FI Fayez Issa
PO Paule Opolon
OB Olivia Bawa
WR Windy Rondof
AM Antonin Marchais
PD Philippe Dessen
GM Guillaume Meurice
ML Morgane Le-Gall
MP Melanie Polrot
KR Karine Ser-Le Roux
KM Kamel Mamchaoui
ND Nathalie Droin
HR Hana Raslova
PM Pascal Maire
BG Birgit Geoerger
IP Iryna Pirozhkova
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RNA-seq libraries from the MAPPYACTS study sequencing data were aligned with the GRCh38 version of the human transcriptome from the GENCODE project using Salmon v0.9 (Patro et al, 2017) and converted from transcripts to gene expression using the Tximport R package. RNA-seq analysis data of 1375 cancer cell lines were extracted from the DepMap Broad Institute portal. The data were then computed using DEBrowser (Kucukural et al, 2019) and the DESeq2 R package (TMM normalization, parametric fit, LRT test). Coexpression analysis was performed using the network_plot R function.

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