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

## Documentation for package ‘derfinder’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

advancedArg | Deprecated functions in package 'derfinder'
analyzeChr | Run the derfinder analysis on a chromosome
annotateRegions | Assign genomic states to regions
calculatePvalues | Calculate p-values and identify regions
calculateStats | Calculate F-statistics at base pair resolution from a loaded BAM files
coerceGR | Coerce the coverage to a GRanges object for a given sample
collapseFullCoverage | Collapse full coverage information for efficient quantile computations
coverageToExon | Extract coverage information for exons
createBw | Export coverage to BigWig files
createBwSample | Create a BigWig file with the coverage information for a given sample
define_cluster | Define a cluster to use.
derfinder-deprecated | Deprecated functions in package 'derfinder'
extendedMapSeqlevels | Change naming style for a set of sequence names
filterData | Filter the positions of interest
findRegions | Find non-zero regions in a Rle
fullCoverage | Load the unfiltered coverage information from a group of BAM files and a list of chromosomes
genomeData | Genome samples processed data
genomeDataRaw | Genome samples processed data
genomeFstats | F-statistics for the example data
genomeInfo | Genome samples information
genomeRegions | Candidate DERs for example data
genomicState | Genomic State for Hsapiens.UCSC.hg19.knownGene
getRegionCoverage | Extract coverage information for a set of regions
getTotalMapped | Calculate the total number of mapped reads
loadCoverage | Load the coverage information from a group of BAM files
makeGenomicState | Obtain the genomic state per region from annotation
makeModels | Build model matrices for differential expression
mergeResults | Merge results from different chromosomes
preprocessCoverage | Transform and split the data
railMatrix | Identify regions data by a coverage filter and get a count matrix from BigWig files
rawFiles | Construct full paths to a group of raw input files
regionMatrix | Identify regions data by a coverage filter and get a count matrix
sampleDepth | Calculate adjustments for library size