Package: MatrixRider 1.44.0

Elena Grassi

MatrixRider: Obtain total affinity and occupancies for binding site matrices on a given sequence

Calculates a single number for a whole sequence that reflects the propensity of a DNA binding protein to interact with it. The DNA binding protein has to be described with a PFM matrix, for example gotten from Jaspar.

Authors:Elena Grassi

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manual.pdf |manual.html✨
card.svg |card.png
MatrixRider/json (API)
NEWS

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

On BioConductor:MatrixRider-1.45.0(bioc 3.24)MatrixRider-1.44.0(bioc 3.23)

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

generegulationgeneticsmotifannotation

3.30 score 8 scripts 384 downloads 1 exports 71 dependencies

Last updated from:6ebda07d84 (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK, 4 WARNING. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR207
linux-devel-arm64NOTE341
linux-devel-x86_64NOTE432
source / vignettesOK363
linux-release-arm64NOTE338
linux-release-x86_64NOTE410
macos-release-arm64WARNING232
macos-release-x86_64WARNING573
macos-oldrel-arm64WARNING189
macos-oldrel-x86_64WARNING467
windows-develNOTE348
windows-releaseNOTE339
windows-oldrelNOTE320
wasm-releaseOK165

Exports:getSeqOccupancy

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcaToolscigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayDirichletMultinomialfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluegtoolshttrIRangesjsonlitelambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpwalignR6RcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfoseqLogosnowSparseArraySummarizedExperimentsysTFBSToolsTFMPvaluevctrsXMLXVectoryaml

Total affinity and occupancies

Rendered fromMatrixRider.Rnwusingutils::Sweaveon May 29 2026.

Last update: 2018-06-23
Started: 2015-03-13

Readme and manuals

Help Manual

Help pageTopics
Calculate total affinity and occupancies for binding site matrices on a given sequenceMatrixRider-package MatrixRider
Computes the total affinity or the occupancy at a given cutoffgetSeqOccupancy getSeqOccupancy,DNAString,PFMatrix,numeric-method getSeqOccupancy,DNAString,PFMatrixList,numeric-method getSeqOccupancy-methods