Analysis scripts for EM ampliseq manuscript
Alexander Predeus, 2016-2018, predeus at gmail dot com
A. V. Predeus, E. S. Vashukova, A. S. Glotov, M. M. Danilova, N. S. Osinovskaya, O. V. Malysheva, N. Yu. Shved, N. Ganbarli, M. I. Yarmolinskaya, T. E. Ivashchenko, V. S. Baranov, Next-Generation Sequencing of Matched Ectopic and Eutopic Endometrium Identifies Novel Endometriosis-Related Genes, Russian Journal of Genetics, 2018, 54(11), 1358–1365.
Raw reads generated by AmpliSeq/IonTorrent program are available via GEO database GSE99949.
Reads were processed using rnaquant pipeline. Resulting matrix of gene expression (raw read counts) was analyzed in R using DESeq2 and fgsea.