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

## Documentation for package ‘derfinder’ version 1.6.4

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

## Help Pages

derfinder-package | Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach.
advancedArg | List advanced arguments
advanced_arg | Defunct functions in package 'derfinder'
analyzeChr | Run the derfinder analysis on a chromosome
analyze_chr | Defunct functions in package 'derfinder'
annotateRegions | Assign genomic states to regions
annotate_regions | Defunct functions in package 'derfinder'
calculatePvalues | Calculate p-values and identify regions
calculateStats | Calculate F-statistics at base pair resolution from a loaded BAM files
calculate_pvalues | Defunct functions in package 'derfinder'
calculate_stats | Defunct functions in package 'derfinder'
coerceGR | Coerce the coverage to a GRanges object for a given sample
coerce_gr | Defunct functions in package 'derfinder'
collapseFullCoverage | Collapse full coverage information for efficient quantile computations
collapse_full_coverage | Defunct functions in package 'derfinder'
coverageToExon | Extract coverage information for exons
coverage_to_exon | Defunct functions in package 'derfinder'
createBw | Export coverage to BigWig files
createBwSample | Create a BigWig file with the coverage information for a given sample
create_bw | Defunct functions in package 'derfinder'
create_bw_sample | Defunct functions in package 'derfinder'
derfinder-defunct | Defunct functions in package 'derfinder'
extendedMapSeqlevels | Change naming style for a set of sequence names
extended_map_seqlevels | Defunct functions in package 'derfinder'
filterData | Filter the positions of interest
filter_data | Defunct functions in package 'derfinder'
findRegions | Find non-zero regions in a Rle
find_regions | Defunct functions in package 'derfinder'
fullCoverage | Load the unfiltered coverage information from a group of BAM files and a list of chromosomes
full_coverage | Defunct functions in package 'derfinder'
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
get_region_coverage | Defunct functions in package 'derfinder'
loadCoverage | Load the coverage information from a group of BAM files
load_coverage | Defunct functions in package 'derfinder'
makeGenomicState | Obtain the genomic state per region from annotation
makeModels | Build model matrices for differential expression
make_genomic_state | Defunct functions in package 'derfinder'
make_models | Defunct functions in package 'derfinder'
mergeResults | Merge results from different chromosomes
merge_results | Defunct functions in package 'derfinder'
preprocessCoverage | Transform and split the data
preprocess_coverage | Defunct functions in package 'derfinder'
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
raw_files | Defunct functions in package 'derfinder'
regionMatrix | Identify regions data by a coverage filter and get a count matrix
region_matrix | Defunct functions in package 'derfinder'
sampleDepth | Calculate adjustments for library size
sample_depth | Defunct functions in package 'derfinder'