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