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derfinder (version 1.6.4)

Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

Description

This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.

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Version

Version

1.6.4

License

Artistic-2.0

Issues

3

Pull Requests

0

Stars

43

Forks

15

Maintainer

Leonardo Collado-Torres

Last Published

February 15th, 2017

Functions in derfinder (1.6.4)

advancedArg

List advanced arguments
analyzeChr

Run the derfinder analysis on a chromosome
createBwSample

Create a BigWig file with the coverage information for a given sample
genomeData

Genome samples processed data
genomeDataRaw

Genome samples processed data
collapseFullCoverage

Collapse full coverage information for efficient quantile computations
findRegions

Find non-zero regions in a Rle
calculateStats

Calculate F-statistics at base pair resolution from a loaded BAM files
vennRegions

Venn diagram for annotated regions given the genomic state
regionMatrix

Identify regions data by a coverage filter and get a count matrix
genomeInfo

Genome samples information
loadCoverage

Load the coverage information from a group of BAM files
coverageToExon

Extract coverage information for exons
railMatrix

Identify regions data by a coverage filter and get a count matrix from BigWig files
coerceGR

Coerce the coverage to a GRanges object for a given sample
makeModels

Build model matrices for differential expression
derfinderHelper-package

derfinder helper package
genomeRegions

Candidate DERs for example data
sampleDepth

Calculate adjustments for library size
plotOverview

Plot a karyotype overview of the genome with the identified regions
filterData

Filter the positions of interest
derfinderPlot-defunct

Defunct functions in package derfinderPlot
createBw

Export coverage to BigWig files
genomeFstats

F-statistics for the example data
makeGenomicState

Obtain the genomic state per region from annotation
mergeResults

Merge results from different chromosomes
fstats.apply

Calculate F-statistics per base by extracting chunks from a DataFrame
genomicState

Genomic State for Hsapiens.UCSC.hg19.knownGene
plotCluster

Plot the coverage information surrounding a region cluster
derfinder-defunct

Defunct functions in package derfinder
rawFiles

Construct full paths to a group of raw input files
getRegionCoverage

Extract coverage information for a set of regions
annotateRegions

Assign genomic states to regions
calculatePvalues

Calculate p-values and identify regions
derfinder-package

Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach.
derfinderPlot-package

Plotting functions for derfinder
fullCoverage

Load the unfiltered coverage information from a group of BAM files and a list of chromosomes
extendedMapSeqlevels

Change naming style for a set of sequence names
preprocessCoverage

Transform and split the data
plotRegionCoverage

Makes plots for every region while summarizing the annotation