Package: motifTestR 1.3.3

Stevie Pederson

motifTestR: Perform key tests for binding motifs in sequence data

Taking a set of sequence motifs as PWMs, test a set of sequences for over-representation of these motifs, as well as any positional features within the set of motifs. Enrichment analysis can be undertaken using multiple statistical approaches. The package also contains core functions to prepare data for analysis, and to visualise results.

Authors:Stevie Pederson [aut, cre]

motifTestR_1.3.3.tar.gz
motifTestR_1.3.3.zip(r-4.5)motifTestR_1.3.3.zip(r-4.4)motifTestR_1.3.3.zip(r-4.3)
motifTestR_1.3.3.tgz(r-4.5-any)motifTestR_1.3.3.tgz(r-4.4-any)motifTestR_1.3.3.tgz(r-4.3-any)
motifTestR_1.3.3.tar.gz(r-4.5-noble)motifTestR_1.3.3.tar.gz(r-4.4-noble)
motifTestR_1.3.3.tgz(r-4.4-emscripten)motifTestR_1.3.3.tgz(r-4.3-emscripten)
motifTestR.pdf |motifTestR.html✨
motifTestR/json (API)
NEWS

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

Bug tracker:https://github.com/smped/motiftestr/issues

Datasets:
  • ar_er_peaks - A set of peaks with AR and ER detected
  • ar_er_seq - Sequences from peaks with AR and ER detected
  • ex_pfm - Example Position Frequency Matrices
  • hg19_mask - Regions from hg19 with high N content
  • zr75_enh - Candidate Enhancer Regions from ZR-75-1 Cells

On BioConductor:motifTestR-1.3.3(bioc 3.21)motifTestR-1.2.1(bioc 3.20)

motifannotationchipseqchiponchipsequencematchingsoftware

4.93 score 1 stars 2 scripts 180 downloads 12 exports 55 dependencies

Last updated 1 months agofrom:b1c54df338. Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 19 2025
R-4.5-winOKFeb 19 2025
R-4.5-macOKFeb 19 2025
R-4.5-linuxOKFeb 19 2025
R-4.4-winOKFeb 19 2025
R-4.4-macOKFeb 19 2025
R-4.3-winOKFeb 19 2025
R-4.3-macOKFeb 19 2025

Exports:clusterMotifscountClusterMatchescountPwmMatchesgetClusterMatchesgetPwmMatchesmakeRMRangesplotMatchPossimSeqtestClusterEnrichtestClusterPostestMotifEnrichtestMotifPos

Dependencies:askpassBiocGenericsBiostringsclicolorspacecrayoncurlfansifarverFMStablegenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtableharmonicmeanphttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigR6RColorBrewerRcppRcppThreadrlangS4VectorsscalessystibbleUCSC.utilsuniversalmotifutf8vctrsviridisLitewithrXVectoryaml

Motif Analysis Using motifTestR

Stevie Pederson

Rendered frommotifAnalysis.Rmdusingknitr::rmarkdownon Feb 19 2025.

Last update: 2025-01-11
Started: 2024-02-28