Package: motifTestR 1.3.1

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_1.3.1.tar.gz
motifTestR_1.3.1.zip(r-4.5)motifTestR_1.3.1.zip(r-4.4)motifTestR_1.3.1.zip(r-4.3)
motifTestR_1.3.1.tgz(r-4.4-any)motifTestR_1.3.1.tgz(r-4.3-any)
motifTestR_1.3.1.tar.gz(r-4.5-noble)motifTestR_1.3.1.tar.gz(r-4.4-noble)
motifTestR_1.3.1.tgz(r-4.4-emscripten)motifTestR_1.3.1.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'))

Peer review:

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-1.3.0(bioc 3.21)motifTestR-1.2.0(bioc 3.20)

motifannotationchipseqchiponchipsequencematchingsoftware

4.90 score 1 stars 2 scripts 181 downloads 11 exports 56 dependencies

Last updated 21 days agofrom:8bd1db5525. Checks:OK: 3 WARNING: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 02 2024
R-4.5-winWARNINGNov 02 2024
R-4.5-linuxWARNINGNov 02 2024
R-4.4-winWARNINGNov 02 2024
R-4.4-macOKNov 02 2024
R-4.3-winWARNINGNov 02 2024
R-4.3-macOKNov 02 2024

Exports:clusterMotifscountClusterMatchescountPwmMatchesgetClusterMatchesgetPwmMatchesmakeRMRangesplotMatchPostestClusterEnrichtestClusterPostestMotifEnrichtestMotifPos

Dependencies:askpassBiocGenericsBiostringsclicolorspacecrayoncurlfansifarverFMStablegenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtableharmonicmeanphttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigR6RColorBrewerRcppRcppThreadrlangS4VectorsscalessystibbleUCSC.utilsuniversalmotifutf8vctrsviridisLitewithrXVectoryamlzlibbioc

Motif Analysis Using motifTestR

Stevie Pederson

Rendered frommotifAnalysis.Rmdusingknitr::rmarkdownon Nov 02 2024.

Last update: 2024-10-16
Started: 2024-02-28