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]

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Rabe.pdf |Rabe.html✨
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 80 dependencies

Last updated 6 months agofrom:22e6ebb929. Checks:7 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 13 2025
R-4.5-win	OK	Feb 13 2025
R-4.5-mac	OK	Feb 13 2025
R-4.5-linux	OK	Feb 13 2025
R-4.4-win	OK	Feb 13 2025
R-4.4-mac	OK	Feb 13 2025
R-4.3-win	OK	Feb 13 2025

Exports:assignToGRanges assignVariantIds diffVariants filterAdenineEditVariants filterVariants getConfidentVariantIds getNameVarTable getVariantTable mergeVariants

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

Adenine base editing analysis

Rendered fromabe-analysis.Rmdusingknitr::rmarkdownon Feb 13 2025.

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