Package: Rabe 0.0.1

Rabe: Adenine base editor analysis

Base editors are emerging molecular sensors for protein-RNA interaction. This package implements a workflow for analysis of adenine base editor datasets. With minimal adjustment it can be used for systematic inquiry of any known single base-pair mutagenesis patterns. Part of the y3628 analysis suite.

Authors:Ye Yuan [aut, cre]

Rabe_0.0.1.tar.gz
Rabe_0.0.1.zip(r-4.7-any)Rabe_0.0.1.zip(r-4.6-any)Rabe_0.0.1.zip(r-4.5-any)
Rabe_0.0.1.tgz(r-4.6-any)Rabe_0.0.1.tgz(r-4.5-any)
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Rabe_0.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
Rabe/json (API)

# Install 'Rabe' in R:

install.packages('Rabe', repos = c('https://yeyuan98.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yeyuan98/rabe/issues

On CRAN:

cellbiology genetics

2.00 score 1 scripts 9 exports 78 dependencies

Last updated from:22e6ebb929. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	154
source / vignettes	OK	221
linux-release-x86_64	OK	171
macos-release-arm64	OK	94
macos-oldrel-arm64	OK	107
windows-devel	OK	104
windows-release	OK	110
windows-oldrel	OK	89
wasm-release	OK	132

Exports:assignToGRanges assignVariantIds diffVariants filterAdenineEditVariants filterVariants getConfidentVariantIds getNameVarTable getVariantTable mergeVariants

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli codetools cpp11 crayon curl DBI DelayedArray dplyr fastmap formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyselect utf8 VariantAnnotation vctrs withr XML XVector yaml

Adenine base editing analysis

Rendered fromabe-analysis.Rmdusingknitr::rmarkdown

Last update: 2024-08-11
Started: 2024-08-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Assign variant IDs to a GRanges object based on overlap	assignToGRanges
Assign overlapping VCF variant IDs to a GRanges	assignVariantIds
Set difference of two variant tables	diffVariants
Filter variants to include only Adenine base editing	filterAdenineEditVariants
Filter a single merged variant table	filterVariants
Get 'confident' variants for downstream analysis	getConfidentVariantIds
Convert GRanges with assigned variants into a tibble	getNameVarTable
Get data frame of primary variants from a VCF file	getPrimaryVariantTable
Return detailed variant information (mutation rate, counts for REF/ALT).	getVariantTable
Merge a list of variant tables into one table.	mergeVariants
Format summary of a numeric vector	prettyFormatSummary
Prune a GenomicRanges containing variants to retain only A->G edits	pruneAdenineEditVariants
Convert A/G variant ID vector into GenomicRanges::GRanges	variantID2GRanges