"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 |
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 |
importFIMO |
import a FIMO bed-like file |
importFIMO-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 |
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 |
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 |
URL_s3_tf |
utility to generate link to biocfound bucket for FIMO TFBS scores |