Package: MatrixRider 1.45.0

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.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 6 scripts 384 downloads 1 exports 72 dependencies

Last updated from:795d12a7a5. Checks:1 ERROR, 7 NOTE, 2 OK, 4 WARNING. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR241
linux-devel-arm64NOTE333
linux-devel-x86_64NOTE430
source / vignettesOK327
linux-release-arm64NOTE345
linux-release-x86_64NOTE420
macos-release-arm64WARNING252
macos-release-x86_64WARNING614
macos-oldrel-arm64WARNING255
macos-oldrel-x86_64WARNING459
windows-develNOTE297
windows-releaseNOTE292
windows-oldrelNOTE313
wasm-releaseOK187

Exports:getSeqOccupancy

Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcaToolscigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayDirichletMultinomialfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluegtoolshttrIRangesjsonlitelambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpwalignR6RcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfoseqLogosnowSparseArraySummarizedExperimentsysTFBSToolsTFMPvaluevctrsXMLXVectoryaml

Total affinity and occupancies

Rendered fromMatrixRider.Rnwusingutils::Sweaveon May 30 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