📦 bitseq

C

• convertSamples(1)convert or normalize MCMC expression samples✨

E

• 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✨

G

• 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✨

P

• parseAlignment(1)pre-compute probabilities of (observed) reads alignments✨

T

• transposeLargeFile(1)helper for bitseq to transpose files lines and columns✨