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| 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 |