Package: branchpointer 1.39.0

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

branchpointer_1.39.0.tar.gz
branchpointer_1.39.0.zip(r-4.7-any)branchpointer_1.39.0.zip(r-4.6-any)branchpointer_1.39.0.zip(r-4.5-any)
branchpointer_1.39.0.tgz(r-4.6-any)branchpointer_1.39.0.tgz(r-4.5-any)
branchpointer_1.39.0.tar.gz(r-4.7-any)branchpointer_1.39.0.tar.gz(r-4.6-any)
branchpointer_1.39.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
branchpointer/json (API)

# Install 'branchpointer' in R:

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

On BioConductor:branchpointer-1.39.0(bioc 3.24)branchpointer-1.38.0(bioc 3.23)

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

software genomeannotation genomicvariation motifannotation

3.72 score 26 scripts 674 downloads 2 mentions 7 exports 137 dependencies

Last updated from:79e9a91a4f. Checks:9 ERROR, 1 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	239
linux-devel	ERROR	447
source / vignettes	ERROR	461
linux-release	ERROR	471
macos-release	ERROR	366
macos-oldrel	ERROR	362
windows-devel	ERROR	313
windows-release	ERROR	389
windows-oldrel	ERROR	391
wasm-release	OK	192

Exports:gtfToExons makeBranchpointWindowForExons makeBranchpointWindowForSNP plotBranchpointWindow predictBranchpoints predictionsToSummary readQueryFile

Dependencies:AnnotationDbi askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob BSgenome BSgenome.Hsapiens.UCSC.hg38 cachem caret cigarillo class cli clock codetools cowplot cpp11 crayon curl data.table DBI dbplyr diagram digest dplyr e1071 farver fastmap filelock foreach formatR futile.logger futile.options future future.apply gbm generics GenomeInfoDb 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 matrixStats memoise mime ModelMetrics nlme nnet numDeriv openssl parallelly pillar pkgconfig plyr png prettyunits pROC prodlim progress progressr proxy purrr R6 RColorBrewer Rcpp RCurl recipes reshape2 restfulr Rhtslib rjson rlang rpart Rsamtools RSQLite rtracklayer S4Vectors S7 scales Seqinfo shape snow sparsevctrs SQUAREM stringi stringr survival sys tibble tidyr tidyselect timechange timeDate tzdb UCSC.utils utf8 vctrs viridisLite withr XML xml2 XVector yaml

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

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