Package: motifTestR 1.1.3
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:
motifTestR_1.1.3.tar.gz
motifTestR_1.1.3.zip(r-4.5)motifTestR_1.1.3.zip(r-4.4)motifTestR_1.1.3.zip(r-4.3)
motifTestR_1.1.3.tgz(r-4.4-any)motifTestR_1.1.3.tgz(r-4.3-any)
motifTestR_1.1.3.tar.gz(r-4.5-noble)motifTestR_1.1.3.tar.gz(r-4.4-noble)
motifTestR_1.1.3.tgz(r-4.4-emscripten)motifTestR_1.1.3.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
- ar_er_peaks - A set of peaks with AR and ER detected
- ar_er_seq - Sequences from peaks with AR and ER detected
- ex_pwm - Example Position Weight Matrices
- hg19_mask - Regions from hg19 with high N content
- zr75_enh - Candidate Enhancer Regions from ZR-75-1 Cells
On BioConductor:motifTestR-1.1.3(bioc 3.20)motifTestR-1.0.3(bioc 3.19)
Last updated 1 months agofrom:f6b82fa45a
Exports:countPwmMatchesgetPwmMatchesmakeRMRangesplotMatchPostestMotifEnrichtestMotifPos
Dependencies:askpassBiocGenericsBiostringsclicolorspacecrayoncurlfansifarverFMStableGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtableharmonicmeanphttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigR6RColorBrewerRcppRcppThreadrlangS4VectorsscalessystibbleUCSC.utilsuniversalmotifutf8vctrsviridisLitewithrXVectoryamlzlibbioc
Readme and manuals
Help Manual
Help page | Topics |
---|---|
A set of peaks with AR and ER detected | ar_er_peaks |
Sequences from peaks with AR and ER detected | ar_er_seq |
Count the matches to a PWM within an XStringSet | countPwmMatches |
Example Position Weight Matrices | ex_pwm |
Find all PWM matches within an XStringSet | getPwmMatches |
Regions from hg19 with high N content | hg19_mask |
Form a set of random, matching ranges for bootstrapping or permuting | makeRMRanges makeRMRanges,GRanges,GRanges-method makeRMRanges,GRangesList,GRangesList-method |
Plot Motif Match Positions | plotMatchPos |
Test motif enrichment using a background set of sequences | testMotifEnrich |
Test for a Uniform Distribution across a set of best matches | testMotifPos |
Candidate Enhancer Regions from ZR-75-1 Cells | zr75_enh |