anchor_pmids            check columns of a dataframe for numerical
                        tokens of 7 or 8 digits and create HTML anchors
                        to pubmed.gov constituting a link to a PMID
browse_gotf_main        use DT::datatable to browse the GO catalogue of
                        human DNA-binding transcription factors in
                        Table S1.A of Lovering et al.
browse_humantfs_main    use DT::datatable to browse the Lambert's Human
                        Transcription Factors repository
browse_lambert_gwaslinks
                        browse several hundred disease-TF associations
                        with hyperlinked PMIDs
browse_lambert_main     use DT::datatable to browse the Lambert table
                        S1
ccbr_cell_url           Update Oct 18 2021
cisbpTFcat              cisbpTFcat: data.frame with information on
                        CISBP TFs for human, retained for
                        reproducibility support; see cisbpTFcat_2.0 for
                        a more recent catalog
cisbpTFcat_2.0          cisbpTFcat_2.0: data.frame with information on
                        CISBP TFs for human, described in PMID 31133749
defaultCircosParms      basic layout parameters for circos
demo_fimo_granges       a list of GRanges instances with TF FIMO scores
                        returned by 'fimo_granges'
directHitsInCISBP       demonstrate interoperation of TF catalog with
                        GWAS catalog
encode690               encode690: DataFrame extending AnnotationHub
                        metadata about ENCODE cell line x TF ranges
fimo_granges            create a list of GRanges for FIMO hits in a
                        GenomicFiles instance, corresponding to a
                        GRanges-based query
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
get_rslocs_38           utility to obtain location etc. for rsids of
                        SNPs
gotf_url                Update Oct 18 2021
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_local_split
                        utility to read FIMO outputs from local
                        resource(cluster), assuming bed text split by
                        chromosome
importFIMO,TabixFile,GRanges-method
                        import a FIMO bed-like file
lambert_snps            lambert_snps is Table S3 of Lambert et al PMID
                        29425488
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
retrieve_gotf_main      acquire the content of Table S1.A from Lovering
                        et al., A GO catalogue of human DNA-binding
                        transcription factors, DOI:
                        https://doi.org/10.1101/2020.10.28.359232
retrieve_humantfs_main
                        acquire the CSV content for table S1 of Lambert
                        et al. Cell 2018 from the Human TFS repository
                        at http://humantfs.ccbr.utoronto.ca
retrieve_lambert_main   acquire the Excel spreadsheet content for table
                        S1 of Lambert et al. Cell 2018, "The Human
                        Transcription Factors"
seqinfo_hg19_chr17      a Seqinfo instance for a chr17 in hg19
setupHIZE               process a gene_attribute_matrix.txt file from
                        harmonizeome into a GeneSetCollection
show,TFCatalog-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
tffamCirc.plot          use a radial plot (by default) for motif stack
tffamCirc.prep          set up list of pfms in motifStack protocol
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
