edgeR code to run in SevenBridges platform, for RNA-seq results. Takes a gene table (unnormalised values) in a form of Control vs Sample. This script is only for samples have no replicate. Dispersion must be hand giver or else 0.045 will be used.
edgeR_noRep.r
....usage.....
CountTable.txt 1. CONTROL 2. SAMPLE
edgeR_noRep.R INPUT_CountTable.txt dispersion FDR_value_up FDR_value_down P_value UP_regulated_file DOWN_regulated_file All_file
Disregulated genes are annotated using R org.Hs.eg.db package, and only Ensembl Gene ID could be used as key
#prepare_countMatrix.pl is to prepare edgeR compatable CountTable.txt from count table results from HTSeq count results.
!This version is only applicable for GRCh38/hg38
edgeR_predict_dispersion.r
EdgeR, requires replication, without replication dispersion cannot be estimated dispersion calculation can be done using housekeeping genes for same cell lines
edgeR dispersion prediction code to run in SevenBridges platform
. prepare count_table for all counts for your cell line: count_matrix.txt
#ENSEMBL_GENE_ID HDMSO HALPHA HBETA H-S-ALPHA H-S-BETA HSOR
#ENSG00000000003 1133 918 953 1185 730 864
#ENSG00000000005 1 0 1 0 0 0
#ENSG00000000419 623 173 349 431 413 527
. prepare ENSEMBL_GENE_ID vs GENE_NAME table for your house keeping genes; house_keeping_genes.txt
#ENSEMBL_GENE_ID GENE_NAME
#ENSG00000128513 POT1
#ENSG00000253729 PRKDC
#ENSG00000168539 CHRM1
#ENSG00000164924 YWHAZ
....usage.....
edgeR_predict_dispersion.R house_keeping_genes.txt count_matrix.txt