Package: TFHAZ 1.29.0

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_1.29.0.tar.gz
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TFHAZ_1.29.0.tgz(r-4.4-any)TFHAZ_1.29.0.tgz(r-4.3-any)
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TFHAZ.pdf |TFHAZ.html✨
TFHAZ/json (API)

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

Peer review:

Datasets:
  • Ishikawa - Contains genomic regions of transcription factors at the ranges side and the name of the transcription factors at the metadata side.
  • 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.
  • base_dense_w_10 - Contains an output of the dense_zones function.
  • reg_dense_w_10 - Contains an output of the dense_zones function.

On BioConductor:TFHAZ-1.29.0(bioc 3.21)TFHAZ-1.28.0(bioc 3.20)

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 200 downloads 7 exports 130 dependencies

Last updated 2 months agofrom:b5ab06bfd4. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 19 2024
R-4.5-winOKDec 19 2024
R-4.5-linuxOKDec 19 2024
R-4.4-winOKDec 19 2024
R-4.4-macOKDec 19 2024
R-4.3-winOKDec 19 2024
R-4.3-macOKDec 19 2024

Exports:accumulationdense_zoneshigh_accumulation_zonesn_zones_PCAplot_accumulationplot_n_zonesw_analysis

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtbiomartrBiostringsbitbit64bitopsblobBSgenomecachemclicliprcodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDESeq2digestdownloaderdplyrfansifarverfastmapfilelockformatRfsfstfstcorefutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtablehmshttrhttr2IRangesisobandjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslORFikphilentropypillarpkgconfigplogrpngpoormanprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRCurlreadrrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttxdbmakertzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLxml2XVectoryamlzlibbioc

TFHAZ

Alberto Marchesi [email protected], Marco Masseroli

Rendered fromTFHAZ.Rmdusingknitr::rmarkdownon Dec 19 2024.

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