HGNCmap                 simple accessor for HGNCmap component of
                        TFCatalog
TFCatalog               Constructor for TFCatalog
TFCatalog-class         define a structure to hold information about
                        TFs from diverse reference sources
TFtargs                 gadget to help sort through tags naming TFs
URL_s3_tf               utility to generate link to biocfound bucket
                        for FIMO TFBS scores
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
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
fimo_granges            create a list of GRanges for FIMO hits in a
                        GenomicFiles instance, corresponding to a
                        GRanges-based query
genemodForGviz          create a GeneRegionTrack instance for selected
                        symbols
genemodelDF             use EnsDb to generate an exon-level model of
                        genes identified by symbol
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
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,TabixFile,GRanges-method
                        import a FIMO bed-like file
importFIMO_local_split
                        utility to read FIMO outputs from local
                        resource(cluster), assuming bed text split by
                        chromosome
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
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
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
