Bitseq

• convertSamples(1) convert or normalize MCMC expression samples
• estimateDE(1) this bitseq module estimates differential expression from data sets
• estimateExpression(1) estimate expression given precomputed probabilities of (observed) reads alignments
• estimateHyperPar(1) estimate expression dependent hyperparameters for bitseq
• estimateVBExpression(1) estimate expression given precomputed probabilities of (observed) reads alignments
• extractSamples(1) extract MCMC samples of selected transcripts
• extractTranscriptInfo(1) extracts information about transcripts from reference Fasta file
• getCounts(1) generate read counts for each input file
• getFoldChange(1) computes log_2 Fold Change from MCMC expression samples
• getGeneExpression(1) compute expression of whole genes
• getPPLR(1) compute PPLR from MCMC expression samples
• getVariance(1) estimates variance of MCMC samples
• getWithinGeneExpression(1) compute relative expression of transcripts within genes
• parseAlignment(1) pre-compute probabilities of (observed) reads alignments
• transposeLargeFile(1) helper for bitseq to transpose files lines and columns