Package: MatrixRider 1.39.0

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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NEWS

# Install 'MatrixRider' in R:

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

On BioConductor:MatrixRider-1.39.0(bioc 3.21)MatrixRider-1.38.0(bioc 3.20)

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

generegulation genetics motifannotation

3.30 score 5 scripts 212 downloads 1 exports 117 dependencies

Last updated 2 months agofrom:bbdf4b1865. Checks:OK: 3 NOTE: 2 WARNING: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win-x86_64	NOTE	Nov 29 2024
R-4.5-linux-x86_64	NOTE	Nov 29 2024
R-4.4-win-x86_64	OK	Nov 29 2024
R-4.4-mac-x86_64	WARNING	Nov 29 2024
R-4.4-mac-aarch64	WARNING	Nov 29 2024
R-4.3-win-x86_64	OK	Nov 29 2024
R-4.3-mac-x86_64	WARNING	Nov 29 2024
R-4.3-mac-aarch64	WARNING	Nov 29 2024

Exports:getSeqOccupancy

Dependencies:abind annotate AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem caTools cli clipr CNEr codetools colorspace cpp11 crayon curl DBI DelayedArray DirichletMultinomial fansi farver fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 glue GO.db gtable gtools hms httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr plyr png poweRlaw pracma prettyunits progress pwalign R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RCurl readr reshape2 restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales seqLogo snow SparseArray stringi stringr SummarizedExperiment sys TFBSTools TFMPvalue tibble tidyselect tzdb UCSC.utils utf8 vctrs viridisLite vroom withr XML xtable XVector yaml zlibbioc

Total affinity and occupancies

Rendered fromMatrixRider.Rnwusingutils::Sweaveon Nov 29 2024.

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

Citation

Development and contributors

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