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| "TFCatalog-class" | define a structure to hold information about TFs from diverse reference sources |
| cisbpTFcat | cisbpTFcat: data.frame with information on CISBP TFs for human |
| directHitsInCISBP | demonstrate interoperation of TF catalog with GWAS catalog |
| encode690 | encode690: DataFrame extending AnnotationHub metadata about ENCODE cell line x TF ranges |
| fimo16 | fimo16: GenomicFiles instance to AWS S3-resident FIMO bed for 16 TFs |
| fimoMap | fimoMap: table with Mnnnn (motif PWM tags) and HGNC symbols for TFs |
| genemodelDF | use EnsDb to generate an exon-level model of genes identified by symbol |
| genemodForGviz | create a GeneRegionTrack instance for selected symbols |
| grabTab | create table of TF targets and related metadata |
| gwascat_hg19_chr17 | gwascat_hg19: GRanges of march 21 2018 EBI gwascat, limit to chr17 |
| HGNCmap | simple accessor for HGNCmap component of TFCatalog |
| hocomoco.mono | hocomoco.mono: data.frame with information on HOCOMOCO TFs for human |
| hocomoco.mono.sep2018 | hocomoco.mono.sep2018: data.frame with information on HOCOMOCO TFs for human, Sept 2018 download |
| importFIMO | import a FIMO bed-like file@importFrom utils read.delim |
| importFIMO-method | import a FIMO bed-like file@importFrom utils read.delim |
| importFIMO_local_split | utility to read FIMO outputs from local resource(cluster), assuming bed text split by chromosome |
| metadata_tf | metadata_tf: list with metadata (motif_if and hgnc_symbol) about all the CISBP FIMO scan TF bed files |
| named_tf | named_tf: named list with the names being the hgnc_symbol of the motif_id |
| setupHIZE | process a gene_attribute_matrix.txt file from harmonizeome into a GeneSetCollection |
| show-method | produce a concise report on TFCatalog instance |
| TFCatalog | Constructor for TFCatalog |
| TFCatalog-class | define a structure to hold information about TFs from diverse reference sources |
| tfhash | tfhash: data.frame with MSigDb TFs, TF targets as symbol or ENTREZ |
| TFtargs | gadget to help sort through tags naming TFs |
| tftColl | tftColl: GSEABase GeneSetCollection for transcription factor targets |
| tftCollMap | tftCollMap: data.frame with information on MSigDb TFs for human |
| topTraitsOfTargets | Use MSigDB TF targets resource to find targets of input TF and find traits to which these targets have been mapped |
| URL_s3_tf | utility to generate link to biocfound bucket for FIMO TFBS scores |