Man pages for ArnaudDroitLab/ef.utils
Eric Utilities

annotate_chipAnnotate "chip.data", given as parameter.
annotate_regionAnnotates a set of regions with genomic features.
annotate_venn_centerAnnotate the inner group of an 'intersect.object'.
annotate_venn_exclusiveAnnotate the outer groups of an 'intersect.object'.
associate_chrom_stateAssociate chromatin sates to a GRanges object.
associate_fitness_genesIdentify essential genes of a GRanges object.
associate_gene_chipAssociate genes to a GRanges object from ChIP-seq data.
associate_genomic_regionAssociate genomic regions to a GRanges object.
associate_histone_marksAssociate histone marks to a GRanges object.
associate_is_gene_activeAssociates a boolean in fonction of the activity of the gene
associate_tfAssociate TF overlaps to a GRanges object.
associate_tissue_specificity_humanAssociate tissue specificity of genes to a GRanges object.
build_intersectGiven a GRangesList object, determine which items overlap...
build_intersect_allBuilds an overlap of the given regions and output all default...
characterize_gene_setGiven a set of Entrez gene ids, perform KEGG enrichment and...
characterize_regionGiven a set of regions, perform annotation, motif enrichment...
chrom_state_matchGiven a set of regions and a chromatin state map, match the...
collapse_regionsCollapses a list of genomic ranges into a single set of...
csaw_analyzeAnalyze bam files with csaw and produces corresponding...
csaw.save.plotsOutput of csaw analysis
default_download_filter_chipDefault filtering function for 'download_encode_chip'.
default_download_filter_rnaDefault filtering function for 'download_encode_rna'.
download_chromatin_statesHelper function for obtaining chromatin states through...
download_encode_chipObtains and process transcription factor data from ENCODE.
download_encode_histonesHelper function for obtaining histone data through...
download_encode_polymerasesHelper function for obtaining polymerase data through...
download_encode_rnaObtains and process expression data from ENCODE.
download_encode_tfHelper function for obtaining transcription factor data...
download.one.chrom.stateDownload a single chromatin state map from ENCODE.
exclusive.overlap.internalInternal exclusive overlap.
filter.reads.to.countsFilter out unintersing windows, by global enrichment method.
gene_from_regionsGiven a set of regions, convert it to a set of Entrez gene...
gene_peaks_distancesGenerate a summary of the distances separating a set of genes...
get.chrom.state.urlGiven a mnemonic and a number of states, builds the download...
get_encode_mnemonicGiven a biosample's name, tries to match it with an ENCODE...
get_promotersGiven a set of Entrez IDS, retrieve the coordinates of those...
histone_download_filter_chipAlternative filtering function for 'download_encode_chip'.
import.and.discard.metadataImport a bed file and discards its metadata.
import_chrom_statesImport HMM chromatin states for the right cell type.
import_files_into_grlImport a set of bed-lie files into a GRangesList.
import_into_grlImport a set of bed files in a directory into a GRangesList.
inclusive.overlap.internalInternal inclusive overlap.
install_annotationsInstall required annotation packages.
intersect_overlapCalculate an overlap of certain factors within an...
intersect_venn_plotGenerates a venn diagram from an 'intersect.object'.
isoform_download_filter_rnaAlternative filtering function for 'download_encode_rna'.
kegg_enrichmentPerform KEGG pathway enrichment on a set of genes.
kegg_enrichment_regionsPerform KEGG enrichment on a set of regions.
load_chrom_stateGiven the name of a bed file containing a chromatin state...
motif_enrichmentGiven a GRanges object, finds enriched motifs within those...
motif_enrichment_genesPerform motif enrichment on the promoters of a set of genes.
multiple_keggs_plotGenerates a plot representing significant kegg pathways from...
multiple_region_enrichmentPerforms region enrichment on a set of regions and returns...
multiple.testingMake corrections for multiple testing
normalization.factorsCalculate normalization factors, by using TMM method.
pairwise_overlapCalculate the pairwise overlaps of all factors within an...
partition_genomic_regionsGenerate a GRanges object partitioning the genome into...
pol2_download_filter_chipAlternative filtering function for 'download_encode_chip'.
post_processingSave results of 'multiple.testing' with annotations
project_rangesProjects the ranges in query into the ranges in target.
read_identicalImport a set of identically structured files.
reads.to.countsConvert reads from bam files to counts
region_consensusObtains consensus regions from a set of regions.
region_enrichmentCalculates enrichment ratios for quer regions against a...
region_enrichment_summaryPerforms a summary of region enrichment results.
region_overlapGenerate a matrix detailing the percentage of overlap between...
select_annotationsAnnotations selection helper.
simple_chrom_state_mapReturns the mapping used to go from full chromatin states to...
simplify_chrom_stateSimplifies chromatin state names.
test.diff.bindingTest the differential binding.
ArnaudDroitLab/ef.utils documentation built on May 28, 2017, 5:54 p.m.