Man pages for vjcitn/TFutils
TFutils

anchor_pmidscheck columns of a dataframe for numerical tokens of 7 or 8...
browse_lambert_gwaslinksbrowse several hundred disease-TF associations with...
browse_lambert_mainuse DT::datatable to browse the Lambert table S1
cisbpTFcatcisbpTFcat: data.frame with information on CISBP TFs for...
cisbpTFcat_2.0cisbpTFcat_2.0: data.frame with information on CISBP TFs for...
defaultCircosParmsbasic layout parameters for circos
demo_fimo_grangesa list of GRanges instances with TF FIMO scores returned by...
directHitsInCISBPdemonstrate interoperation of TF catalog with GWAS catalog
encode690encode690: DataFrame extending AnnotationHub metadata about...
fimo16fimo16: GenomicFiles instance to AWS S3-resident FIMO bed for...
fimo_grangescreate a list of GRanges for FIMO hits in a GenomicFiles...
fimoMapfimoMap: table with Mnnnn (motif PWM tags) and HGNC symbols...
genemodelDFuse EnsDb to generate an exon-level model of genes identified...
genemodForGvizcreate a GeneRegionTrack instance for selected symbols
get_rslocs_38utility to obtain location etc. for rsids of SNPs
grabTabcreate table of TF targets and related metadata
gwascat_hg19_chr17gwascat_hg19: GRanges of march 21 2018 EBI gwascat, limit to...
HGNCmapsimple accessor for HGNCmap component of TFCatalog
hocomoco.monohocomoco.mono: data.frame with information on HOCOMOCO TFs...
hocomoco.mono.sep2018hocomoco.mono.sep2018: data.frame with information on...
importFIMOimport a FIMO bed-like [email protected] utils read.delim
importFIMO_local_splitutility to read FIMO outputs from local resource(cluster),...
lambert_snpslambert_snps is Table S3 of Lambert et al PMID 29425488
metadata_tfmetadata_tf: list with metadata (motif_if and hgnc_symbol)...
named_tfnamed_tf: named list with the names being the hgnc_symbol of...
retrieve_lambert_mainacquire the Excel spreadsheet content for table S1 of Lambert...
seqinfo_hg19_chr17a Seqinfo instance for a chr17 in hg19
setupHIZEprocess a gene_attribute_matrix.txt file from harmonizeome...
show-TFCatalog-methodproduce a concise report on TFCatalog instance
TFCatalogConstructor for TFCatalog
TFCatalog-classdefine a structure to hold information about TFs from diverse...
tffamCirc.plotuse a radial plot (by default) for motif stack
tffamCirc.prepset up list of pfms in motifStack protocol
tfhashtfhash: data.frame with MSigDb TFs, TF targets as symbol or...
TFtargsgadget to help sort through tags naming TFs
tftColltftColl: GSEABase GeneSetCollection for transcription factor...
tftCollMaptftCollMap: data.frame with information on MSigDb TFs for...
topTraitsOfTargetsUse MSigDB TF targets resource to find targets of input TF...
URL_s3_tfutility to generate link to biocfound bucket for FIMO TFBS...
vjcitn/TFutils documentation built on Aug. 31, 2019, 7:58 p.m.