Package: TFutils 1.27.1

Vincent Carey

TFutils: TFutils

This package helps users to work with TF metadata from various sources. Significant catalogs of TFs and classifications thereof are made available. Tools for working with motif scans are also provided.

Authors:Vincent Carey [aut, cre], Shweta Gopaulakrishnan [aut]

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TFutils.pdf |TFutils.html✨
TFutils/json (API)
NEWS

# Install 'TFutils' in R:
install.packages('TFutils', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • 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
  • demo_fimo_granges - A list of GRanges instances with TF FIMO scores returned by 'fimo_granges'
  • 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
  • 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
  • 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
  • seqinfo_hg19_chr17 - A Seqinfo instance for a chr17 in hg19
  • 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

On BioConductor:TFutils-1.27.0(bioc 3.21)TFutils-1.26.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

transcriptomics

4.76 score 19 scripts 236 downloads 1 mentions 25 exports 125 dependencies

Last updated 9 days agofrom:6c536519cd. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 13 2024
R-4.5-winERRORNov 13 2024
R-4.5-linuxERRORNov 13 2024
R-4.4-winERRORNov 13 2024
R-4.4-macERRORNov 13 2024
R-4.3-winERRORNov 13 2024
R-4.3-macERRORNov 13 2024

Exports:anchor_pmidsbrowse_gotf_mainbrowse_humantfs_mainbrowse_lambert_gwaslinksbrowse_lambert_maindefaultCircosParmsdirectHitsInCISBPfimo_grangesgenemodelDFgenemodForGvizget_rslocs_38grabTabHGNCmapimportFIMOimportFIMO_local_splitretrieve_gotf_mainretrieve_humantfs_mainretrieve_lambert_mainshowTFCatalogtffamCirc.plottffamCirc.prepTFtargstopTraitsOfTargetsURL_s3_tf

Dependencies:abindannotateAnnotationDbiaskpassbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomebslibcachemcellrangerclicodetoolscommonmarkcpp11crayoncrosstalkcurlDBIdbplyrDelayedArraydigestdplyrDTevaluatefansifastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicRangesgluegraphGSEABasehighrhmshtmltoolshtmlwidgetshttpuvhttrIRangesjquerylibjsonliteKEGGRESTknitrlambda.rlaterlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeminiUIopensslorg.Hs.eg.dbpillarpkgconfigplogrpngprettyunitsprogresspromisespurrrR6rappdirsRcppRCurlreadxlrematchrestfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassshinysnowsourcetoolsSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrswithrxfunXMLxtableXVectoryamlzlibbioc

A note on fimo16 in TFutils

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered fromfimo16.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2024-11-12
Started: 2019-07-01

TFutils: Data Structures for Transcription Factor Bioinformatics

BJ Stubbs, Shweta Gopaulakrishnan, Kimberly Glass, Nathalie Pochet, Celine Everaert, Benjamin Raby, Vincent Carey

Rendered fromTFutils.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2018-09-03
Started: 2018-03-27

Readme and manuals

Help Manual

Help pageTopics
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 PMIDanchor_pmids
use DT::datatable to browse the GO catalogue of human DNA-binding transcription factors in Table S1.A of Lovering et al.browse_gotf_main
use DT::datatable to browse the Lambert's Human Transcription Factors repositorybrowse_humantfs_main
browse several hundred disease-TF associations with hyperlinked PMIDsbrowse_lambert_gwaslinks
use DT::datatable to browse the Lambert table S1browse_lambert_main
Update Oct 18 2021ccbr_cell_url
cisbpTFcat: data.frame with information on CISBP TFs for human, retained for reproducibility support; see cisbpTFcat_2.0 for a more recent catalogcisbpTFcat
cisbpTFcat_2.0: data.frame with information on CISBP TFs for human, described in PMID 31133749cisbpTFcat_2.0
basic layout parameters for circosdefaultCircosParms
a list of GRanges instances with TF FIMO scores returned by 'fimo_granges'demo_fimo_granges
demonstrate interoperation of TF catalog with GWAS catalogdirectHitsInCISBP
encode690: DataFrame extending AnnotationHub metadata about ENCODE cell line x TF rangesencode690
create a list of GRanges for FIMO hits in a GenomicFiles instance, corresponding to a GRanges-based queryfimo_granges
fimo16: GenomicFiles instance to AWS S3-resident FIMO bed for 16 TFsfimo16
fimoMap: table with Mnnnn (motif PWM tags) and HGNC symbols for TFsfimoMap
use EnsDb to generate an exon-level model of genes identified by symbolgenemodelDF
create a GeneRegionTrack instance for selected symbolsgenemodForGviz
utility to obtain location etc. for rsids of SNPsget_rslocs_38
Update Oct 18 2021gotf_url
create table of TF targets and related metadatagrabTab
gwascat_hg19: GRanges of march 21 2018 EBI gwascat, limit to chr17gwascat_hg19_chr17
simple accessor for HGNCmap component of TFCatalogHGNCmap
hocomoco.mono: data.frame with information on HOCOMOCO TFs for humanhocomoco.mono
hocomoco.mono.sep2018: data.frame with information on HOCOMOCO TFs for human, Sept 2018 downloadhocomoco.mono.sep2018
utility to read FIMO outputs from local resource(cluster), assuming bed text split by chromosomeimportFIMO_local_split
import a FIMO bed-like fileimportFIMO importFIMO,character,missing-method importFIMO,TabixFile,GRanges-method
lambert_snps is Table S3 of Lambert et al PMID 29425488lambert_snps
metadata_tf: list with metadata (motif_if and hgnc_symbol) about all the CISBP FIMO scan TF bed filesmetadata_tf
named_tf: named list with the names being the hgnc_symbol of the motif_idnamed_tf
acquire the content of Table S1.A from Lovering et al., A GO catalogue of human DNA-binding transcription factors, DOI: https://doi.org/10.1101/2020.10.28.359232retrieve_gotf_main
acquire the CSV content for table S1 of Lambert et al. Cell 2018 from the Human TFS repository at http://humantfs.ccbr.utoronto.caretrieve_humantfs_main
acquire the Excel spreadsheet content for table S1 of Lambert et al. Cell 2018, "The Human Transcription Factors"retrieve_lambert_main
a Seqinfo instance for a chr17 in hg19seqinfo_hg19_chr17
process a gene_attribute_matrix.txt file from harmonizeome into a GeneSetCollectionsetupHIZE
produce a concise report on TFCatalog instanceshow,TFCatalog-method
Constructor for TFCatalogTFCatalog
define a structure to hold information about TFs from diverse reference sources"TFCatalog-class" TFCatalog-class
use a radial plot (by default) for motif stacktffamCirc.plot
set up list of pfms in motifStack protocoltffamCirc.prep
tfhash: data.frame with MSigDb TFs, TF targets as symbol or ENTREZtfhash
gadget to help sort through tags naming TFsTFtargs
tftColl: GSEABase GeneSetCollection for transcription factor targetstftColl
tftCollMap: data.frame with information on MSigDb TFs for humantftCollMap
Use MSigDB TF targets resource to find targets of input TF and find traits to which these targets have been mappedtopTraitsOfTargets
utility to generate link to biocfound bucket for FIMO TFBS scoresURL_s3_tf