derfinder-package


Fast differential expression analysis of RNA-seq data at base-pair
resolution from multiple samples. The analysis pipeline involves loading the
sample BAM files using <a rd-options="" href="/link/rawFiles?package=derfinder&version=1.0.10" data-mini-rdoc="derfinder::rawFiles">rawFiles</a> and <a rd-options="" href="/link/loadCoverage?package=derfinder&version=1.0.10" data-mini-rdoc="derfinder::loadCoverage">loadCoverage</a>,
pre-processing the data by using <a rd-options="" href="/link/preprocessCoverage?package=derfinder&version=1.0.10" data-mini-rdoc="derfinder::preprocessCoverage">preprocessCoverage</a>, calculating the
F-statistics (while adjusting for some confounders) using <a rd-options="" href="/link/makeModels?package=derfinder&version=1.0.10" data-mini-rdoc="derfinder::makeModels">makeModels</a>
and <a rd-options="" href="/link/calculateStats?package=derfinder&version=1.0.10" data-mini-rdoc="derfinder::calculateStats">calculateStats</a>, calculating the p-values and finding the regions
of interest using <a rd-options="" href="/link/calculatePvalues?package=derfinder&version=1.0.10" data-mini-rdoc="derfinder::calculatePvalues">calculatePvalues</a>, and finally annotating them using
<a rd-options="bumphunter" href="/link/annotateNearest?package=derfinder&version=1.0.10&to=bumphunter" data-mini-rdoc="bumphunter::annotateNearest">annotateNearest</a> from the bumphunter package.


package

Annotation-agnostic differential expression analysis of RNA-seq
data by calculating F-statistics at base-pair resolution

Leonardo Collado-Torres

derfinder

Annotation-agnostic differential expression analysis of RNA-seq
data at base-pair resolution

derfinder-package function


Fast differential expression analysis of RNA-seq data at base-pair
resolution from multiple samples. The analysis pipeline involves loading the
sample BAM files using <a rd-options='' href='rawFiles'>rawFiles</a> and <a rd-options='' href='loadCoverage'>loadCoverage</a>,
pre-processing the data by using <a rd-options='' href='preprocessCoverage'>preprocessCoverage</a>, calculating the
F-statistics (while adjusting for some confounders) using <a rd-options='' href='makeModels'>makeModels</a>
and <a rd-options='' href='calculateStats'>calculateStats</a>, calculating the p-values and finding the regions
of interest using <a rd-options='' href='calculatePvalues'>calculatePvalues</a>, and finally annotating them using
<a rd-options='bumphunter' href='annotateNearest'>annotateNearest</a> from the bumphunter package.


derfinder-package: Fast differential expression analysis of RNA-seq data at base-pair resolution

Description

Arguments

References