1 Introduction | 2 Looking for binding potential for a single TF on a sequence | 3 Working with multiple matrixes | 4 Appendix A
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:
MatrixRider_1.45.0.tar.gz
MatrixRider_1.45.0.zip(r-4.7)MatrixRider_1.45.0.zip(r-4.6)MatrixRider_1.45.0.zip(r-4.5)
MatrixRider_1.45.0.tgz(r-4.6-x86_64)MatrixRider_1.45.0.tgz(r-4.6-arm64)MatrixRider_1.45.0.tgz(r-4.5-x86_64)MatrixRider_1.45.0.tgz(r-4.5-arm64)
MatrixRider_1.45.0.tar.gz(r-4.7-arm64)MatrixRider_1.45.0.tar.gz(r-4.7-x86_64)MatrixRider_1.45.0.tar.gz(r-4.6-arm64)MatrixRider_1.45.0.tar.gz(r-4.6-x86_64)
MatrixRider_1.45.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MatrixRider/json (API)
| # 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
Last updated from:795d12a7a5. Checks:1 ERROR, 7 NOTE, 2 OK, 4 WARNING. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 214 | ||
| linux-devel-arm64 | NOTE | 310 | ||
| linux-devel-x86_64 | NOTE | 375 | ||
| source / vignettes | OK | 312 | ||
| linux-release-arm64 | NOTE | 325 | ||
| linux-release-x86_64 | NOTE | 391 | ||
| macos-release-arm64 | WARNING | 211 | ||
| macos-release-x86_64 | WARNING | 470 | ||
| macos-oldrel-arm64 | WARNING | 199 | ||
| macos-oldrel-x86_64 | WARNING | 430 | ||
| windows-devel | NOTE | 266 | ||
| windows-release | NOTE | 327 | ||
| windows-oldrel | NOTE | 304 | ||
| wasm-release | OK | 201 |
Exports:getSeqOccupancy
Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcaToolscigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayDirichletMultinomialfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluegtoolshttrIRangesjsonlitelambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpwalignR6RcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfoseqLogosnowSparseArraySummarizedExperimentsysTFBSToolsTFMPvaluevctrsXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate total affinity and occupancies for binding site matrices on a given sequence | MatrixRider-package MatrixRider |
| Computes the total affinity or the occupancy at a given cutoff | getSeqOccupancy getSeqOccupancy,DNAString,PFMatrix,numeric-method getSeqOccupancy,DNAString,PFMatrixList,numeric-method getSeqOccupancy-methods |
