Computational biology and genomics
Lincoln Stein has written a bunch of modules to deal with SAM/BAM files. Check out the CPAN module. If you are having trouble installing Bio::DB::Sam, you may have to recompile SAMTools with the following command: To install the Perl module on a machine where you don’t have root access, follow these instructions. Using this module,…
Updated 2024 August 5th edgeR carries out: Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types…
6th April 2012: For a more updated version of this post, please refer see this post. A very simple comparison Using the TagSeqExample.tab file from the DESeq package as the benchmark dataset. According to DESeq authors, T1a and T1b are similar, so I removed the second column in the file corresponding to T1a: Hierarchical clustering…
Code taken from the DESeq vignette for my own convenience. library(“DESeq”) exampleFile = system.file (“extra/TagSeqExample.tab”,package=”DESeq”) countsTable = read.delim(exampleFile, header=TRUE, stringsAsFactors=TRUE) rownames(countsTable) = countsTable$gene countsTable = countsTable[ , -1] conds = c(“T”,”T”,”T”,”Tb”,”N”,”N”) cds = newCountDataSet (countsTable, conds) cds = cds[,-1] cds = estimateSizeFactors(cds) sizeFactors(cds) cds <- estimateVarianceFunctions( cds ) res <- nbinomTest( cds, “N”, “T” )…