Changes in version 1.13.1 o Functions to manipulate GmtList objects are considerably expanded o All documents and namespaces are now managed by roxygen2 o readGmt by default read unique genes from GMT files Changes in version 1.1-5 o Add C-level implementation of Wilcoxon-Mann-Whitney rank sum test o Documentation and vignettes updated to be ready for Bioconductor submission. Changes in version 1.1-0 o Dependencies on BIOS has been resolved by copying the C functions into the package, in order to prepare BioQC for public release. It can now be installed on systems where BIOS is not available. o Clean-ups and updates of documentations. Changes in version 1.0-14 o Add a series of functions related to Shannon entropy: entropy, entropyDiversity, entropySpecificity, sampleSpecialization Changes in version 1.0-13 o Add gini, a function to calculate Gini index. It implements the gini_stat function in the BIOS library Changes in version 1.0-12 o If the p-value is lower than than the threshold of R (about 10E-320) and thus produces a score of -Inf, the value of 320 is used to avoid -Inf as output. Changes in version 1.0-11 o bioqc.Rscript: add command-line option '-appendGmtDesc' to append DESC column in the GMT file to outputs. Changes in version 1.0-10 o bioqc.Rscript: add details in the help information of 'chiptype' option o bioqc.Rscript: accepts 'GeneID' and 'GeneSymbol' as chiptype in a case-insensitive manner o Update the gmt file to include a few rat tissues (upstream change by Laura Badi, Sep. 3, 2012) Changes in version 1.0-9 o bioqc.Rscript: the threshold input is first transformed by 10^(-threshold) to make inputting threshold easier Changes in version 1.0-8 o filterPmat fixes the warning message when threshold is NULL: it is tested before is.na Changes in version 1.0-7 o bioqc.Rscript rounds output to two digits Changes in version 1.0-6 o Add absLog10p function to take the absolute base-10 logarithm of p-values o Add filterPmat Changes in version 1.0-5 o bioqc.Rscript accepts -gmt correctly (before it is -gmtfile) Changes in version 1.0-4 o exp.tissuemark.affy.roche.symbols.gmt were updated by L. Badi, removing suspected contaminated samples o bioqc.Rscript maps genes to human orthologues from ChipFetcher-exported files Changes in version 1.0-3 o bioqc.Rscript: the dependence on ribiosAnnotation has been simplified: only when chiptype is GeneSymbol, the script does not need ribiosAnnotation o bioqc.Rscript: annotate GeneID and Probesets have been simplified by using syntax from ribiosAnnotation >= 2.0-0 o bioqc.Rscript: Program exists when no valid GeneSymbol could be found. Changes in version 1.0-2 o bioqc.Rscript: Fix supported.ct2 bug seen on the UDIS machine o bioqc.Rscript: ribiosIO minimum version 1.0-12 added Changes in version 1.0-1 o wmw.test has been made more robust: in case no TRUE exists in sub, the function does not fail and return 0 (statistic) or 1 (p-value) o bioqc.Rscript has been added and published under /SOFT/bi/apps/ribios/scripts Changes in version 1.0-0 o Establish the BioQC package o Add methods wmwTest for Wilcoxon-Mann-Whitney test for several data structures used by BIO-QC procedures o wmwTest was (almost) fully documented Changes in version 0.99.4 o wmw_test (C function) is refactored Changes in version 0.99-1 o read_gmt checks whether a GMT line is valid; if not, it prints warning message to the error console and skips the line. o Add following alternatives to wmwTest in order to make the downstream analysis easier: abs.log10.greater, log10.less, abs.log10.two.sided, and Q. o Two.sided tests return correct value if the gene set is of length 0 Changes in version 0.99-0 o Reset the version to 0.99-0 for submission