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