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)branchpointer_1.39.0.zip(r-4.6)branchpointer_1.39.0.zip(r-4.5)
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

4.89 score 26 scripts 439 downloads 2 mentions 7 exports 144 dependencies

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

Target	Result	Time
bioc-checks	ERROR	299
linux-devel-x86_64	OK	595
source / vignettes	OK	549
linux-release-x86_64	OK	546
macos-release-arm64	OK	325
macos-oldrel-arm64	OK	434
windows-devel	OK	556
windows-release	OK	548
windows-oldrel	OK	485
wasm-release	OK	258

Exports:gtfToExons makeBranchpointWindowForExons makeBranchpointWindowForSNP plotBranchpointWindow predictBranchpoints predictionsToSummary readQueryFile

Dependencies:abind 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 DelayedArray 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 MatrixGenerics matrixStats memoise mime ModelMetrics nlme nnet numDeriv openssl parallelly pillar pkgconfig 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 S7 scales Seqinfo shape snow SparseArray sparsevctrs SQUAREM stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timechange timeDate tzdb UCSC.utils utf8 vctrs viridisLite withr XML xml2 XVector yaml

Using Branchpointer for annotation of intronic human splicing branchpoints

Rendered frombranchpointer.Rnwusingknitr::knitr

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