Package: TFHAZ 1.35.0

Gaia Ceddia

TFHAZ: Transcription Factor High Accumulation Zones

It finds trascription factor (TF) high accumulation DNA zones, i.e., regions along the genome where there is a high presence of different transcription factors. Starting from a dataset containing the genomic positions of TF binding regions, for each base of the selected chromosome the accumulation of TFs is computed. Three different types of accumulation (TF, region and base accumulation) are available, together with the possibility of considering, in the single base accumulation computing, the TFs present not only in that single base, but also in its neighborhood, within a window of a given width. Two different methods for the search of TF high accumulation DNA zones, called "binding regions" and "overlaps", are available. In addition, some functions are provided in order to analyze, visualize and compare results obtained with different input parameters.

Authors:Alberto Marchesi, Silvia Cascianelli, Marco Masseroli

TFHAZ_1.35.0.tar.gz
TFHAZ_1.35.0.zip(r-4.7)TFHAZ_1.35.0.zip(r-4.6)TFHAZ_1.35.0.zip(r-4.5)
TFHAZ_1.35.0.tgz(r-4.6-any)TFHAZ_1.35.0.tgz(r-4.5-any)
TFHAZ_1.35.0.tar.gz(r-4.7-any)TFHAZ_1.35.0.tar.gz(r-4.6-any)
TFHAZ_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
TFHAZ/json (API)

# Install 'TFHAZ' in R:
install.packages('TFHAZ', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • base_dense_w_10 - Contains an output of the dense_zones function.
  • Ishikawa - Contains genomic regions of transcription factors at the ranges side and the name of the transcription factors at the metadata side.
  • reg_dense_w_10 - Contains an output of the dense_zones function.
  • TF_acc_w_0 - Contains an output of the accumulation function.
  • TF_dense_w_0 - Contains an output of the dense_zones function.
  • TF_dense_w_10 - Contains an output of the dense_zones function.
  • TF_dense_w_100 - Contains an output of the dense_zones function.
  • TF_dense_w_1000 - Contains an output of the dense_zones function.
  • TF_dense_w_10000 - Contains an output of the dense_zones function.

On BioConductor:TFHAZ-1.35.0(bioc 3.24)TFHAZ-1.34.0(bioc 3.23)

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

softwarebiologicalquestiontranscriptionchipseqcoverage

4.00 score 2 scripts 444 downloads 7 exports 128 dependencies

Last updated from:05269b1e18. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR197
linux-devel-x86_64WARNING406
source / vignettesOK313
linux-release-x86_64WARNING460
macos-release-arm64WARNING254
macos-oldrel-arm64WARNING241
windows-develWARNING349
windows-releaseWARNING323
windows-oldrelWARNING335
wasm-releaseOK185

Exports:accumulationdense_zoneshigh_accumulation_zonesn_zones_PCAplot_accumulationplot_n_zonesw_analysis

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtbiomartrBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicliprcodetoolscowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDESeq2digestdownloaderdplyrfarverfastmapfilelockformatRfsfstfstcorefutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehmshttrhttr2IRangesisobandjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslORFikphilentropypillarpkgconfigpngpoormanprettyunitsprogresspurrrqs2R.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppParallelRCurlreadrrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringfishstringistringrSummarizedExperimentsystibbletidyrtidyselecttxdbmakertzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLxml2XVectoryaml

TFHAZ

Alberto Marchesi [email protected], Marco Masseroli

Rendered fromTFHAZ.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2022-08-05
Started: 2017-07-26