Package: branchpointer 1.33.0

Beth Signal

branchpointer: Prediction of intronic splicing branchpoints

Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs.

Authors:Beth Signal

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branchpointer/json (API)
NEWS

# Install 'branchpointer' in R:

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

On BioConductor:branchpointer-1.31.0(bioc 3.20)branchpointer-1.30.0(bioc 3.19)

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

software genomeannotation genomicvariation motifannotation

4.30 score 20 scripts 228 downloads 7 exports 146 dependencies

Last updated 23 days agofrom:7492c70e09. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	OK	Oct 30 2024
R-4.5-linux	OK	Oct 30 2024
R-4.4-win	OK	Oct 30 2024
R-4.4-mac	OK	Oct 30 2024
R-4.3-win	OK	Oct 30 2024
R-4.3-mac	OK	Oct 30 2024

Exports:gtfToExons makeBranchpointWindowForExons makeBranchpointWindowForSNP plotBranchpointWindow predictBranchpoints predictionsToSummary readQueryFile

Dependencies:abind AnnotationDbi askpass BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob BSgenome BSgenome.Hsapiens.UCSC.hg38 cachem caret class cli clock codetools colorspace cowplot cpp11 crayon curl data.table DBI dbplyr DelayedArray diagram digest dplyr e1071 fansi farver fastmap filelock foreach formatR futile.logger futile.options future future.apply gbm generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 globals glue gower gtable hardhat hms httr httr2 ipred IRanges isoband iterators jsonlite KEGGREST kernlab KernSmooth labeling lambda.r lattice lava lifecycle listenv lubridate magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime ModelMetrics munsell nlme nnet numDeriv openssl parallelly pillar pkgconfig plogr plyr png prettyunits pROC prodlim progress progressr proxy purrr R6 rappdirs RColorBrewer Rcpp RCurl recipes reshape2 restfulr Rhtslib rjson rlang rpart Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales shape snow SparseArray SQUAREM stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timechange timeDate tzdb UCSC.utils utf8 vctrs viridisLite withr XML xml2 XVector yaml zlibbioc

Using Branchpointer for annotation of intronic human splicing branchpoints

Rendered frombranchpointer.Rnwusingknitr::knitron Oct 30 2024.

Last update: 2017-07-11
Started: 2017-03-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Convert GTF file to exon location file	gtfToExons
Make branchpoint window regions	makeBranchpointWindowForExons
Makes a branchpointer formatted GRanges object from refsnp ids	makeBranchpointWindowForSNP
Plots branchpointer predictions	plotBranchpointWindow
Predict branchpoint probability scores	predictBranchpoints
Convert SNP branchpoint predictions across the branchpoint window to an intronic summary	predictionsToSummary
Read a query file	readQueryFile