This is a joint work with Roderic Guigó’s group – Bioinformatics and Genomics program, Center for Genomic Regulatio (CRG). This R package is designed to compare transcript relative expression of different conditions obtained from RNA-seq experiments. Our approach is based on a distance-based non-parametric multivariate ANOVA method.
The Linux version of the package is currently under development. To install a beta version of rasp, start R and enter:
The performance of our approach has been compared with two other existing R packages (`DEXseq` and `EBseq`) using data from The Cancer Genome Atlas (TCGA). Exon abundances from RNA-seq data were obtained for several individuals diagnosed with Liver hepatocellular carcinoma [LIHC] and Bladder Urothelial Carcinoma [BLCA]. We have created two experimental data packages (`ExonCountDataLIHC` and `ExonCountDataBLCA`, respectively). So far, they can be installed by starting R and entering: