Man pages for leekgroup/derfinder
Differential expression analysis of RNA-seq data at base-pair resolution

derfinder-packageDifferential expression analysis of RNA-seq data at base-pair...
findclosest.aheadFind closest long region downstream
findclosest.behindFind closest long region upstream
find.meanOptional helper function for getParams
find.mean.downHelper function for getParams
find.mean.upHelper function for getParams
find.sdHelper function for getParams
getAnnotationDownload exon information for a given genome
getColmedsCalculate the medians of the database.
getExonsFind closest exon(s) to a genomic region
getFF statistic from comparing nested limma models
getFlagsFlag regions with genomic events of interest
getLimmaInputFit a linear model to each nucleotide
getLimmaInput.DFFit a linear model to each nucleotide
get.numaltsHelper function for getParams
getParamsCalculate parameters to use as input for HMM
getParams.failsafeHelper function for getParams
get.pvalsPermutation-based significance tests for differentially...
get.pvals.DFPermutation-based significance tests for differentially...
getRegionsGenerate list of regions, classify each as differentially...
getSvsDo SVA on matrix stored in database
getTstatsCalculate moderated t statistic for each nucleotide
gsubfnHelper function for read.csv.sql
lastGet the last element
locfdrFitModified version of Efron's locfdr
makeDbCreate SQLite database from text file
makeDFMerge the coverage information for a group of samples
match.funfnGeneric extended version of R
mergeRegionsMerge close regions
ostrapplyHelper function for read.csv.sql
plotExonPlot pipeline data/results for a given exon
plotGenePlot pipeline data/results for a given gene
plotRegionPlot pipeline data/results for a given region
read.csv.sqlMain workhorse of makeDb
sqldfHelper function for read.csv.sql
strapplyHelper function for read.csv.sql
supportedTablesPrint list of supported (downloadable) tables for a given...
leekgroup/derfinder documentation built on May 21, 2017, 10:36 a.m.