Package: rnaEditr 1.15.0

Lanyu Zhang

rnaEditr: Statistical analysis of RNA editing sites and hyper-editing regions

RNAeditr analyzes site-specific RNA editing events, as well as hyper-editing regions. The editing frequencies can be tested against binary, continuous or survival outcomes. Multiple covariate variables as well as interaction effects can also be incorporated in the statistical models.

Authors:Lanyu Zhang [aut, cre], Gabriel Odom [aut], Tiago Silva [aut], Lissette Gomez [aut], Lily Wang [aut]

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rnaEditr.pdf |rnaEditr.html✨
rnaEditr/json (API)
NEWS

# Install 'rnaEditr' in R:

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

Bug tracker:https://github.com/transbioinfolab/rnaeditr/issues

Datasets:

rnaedit_df - Example breast cancer RNA editing dataset.
t_rnaedit_df - Transposed breast cancer example dataset.

On BioConductor:rnaEditr-1.15.0(bioc 3.20)rnaEditr-1.14.0(bioc 3.19)

bioconductor-package

27 exports 0.49 score 127 dependencies

Last updated 2 months agofrom:0d74af7d67

Exports:AddMetaData AllCloseByRegions AllCoeditedRegions AnnotateResults CountSamplesPerGroup CreateEditingTable CreateOutputDF CreateRdrop FindCorrelatedRegions GetMinPairwiseCor GetSitesLocations MakeModelFormula MarkCoeditedSites MaxSites MeanSites MedianSites OrderSitesByLocation PC1Sites PlotEditingCorrelations SingleCloseByRegion SingleCoeditedRegion SitesToRegion SummarizeAllRegions SummarizeSingleRegion TestAssociations TestSingleRegion TransformToGR

Dependencies:abind AnnotationDbi askpass backports BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob boot broom bumphunter cachem cli clipr codetools corrplot cpp11 crayon curl DBI DelayedArray digest doRNG dplyr fansi fastmap forcats foreach formatR formula.tools futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glmnet glue haven hms httr IRanges iterators jomo jsonlite KEGGREST lambda.r lattice lifecycle limma lme4 locfit logistf magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mice mime minqa mitml nlme nloptr nnet numDeriv openssl operator.tools ordinal pan pillar pkgconfig plogr plyr png prettyunits progress purrr R6 Rcpp RcppEigen RCurl readr restfulr Rhtslib rjson rlang rngtools rpart Rsamtools RSQLite rtracklayer S4Arrays S4Vectors shape snow SparseArray statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tzdb ucminf UCSC.utils utf8 vctrs vroom withr XML XVector yaml zlibbioc

Introduction to rnaEditr

Lanyu Zhang, Gabriel Odom, Lily Wang

Rendered fromintroduction_to_rnaEditr.Rmdusingknitr::rmarkdownon Jul 01 2024.

Last update: 2020-10-07
Started: 2020-09-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Extract clusters of RNA editing sites located closely in genomic regions.	AllCloseByRegions
Extracts contiguous co-edited genomic regions from input genomic regions .	AllCoeditedRegions
Add Annotations to site-specific or region-based analysis results.	AnnotateResults
Convert RNA editing matrix into a special data frame with class 'rnaEdit_df'.	CreateEditingTable
Example breast cancer RNA editing dataset.	rnaedit_df
Summarize RNA editing levels from multiple sites in regions.	SummarizeAllRegions
Transposed breast cancer example dataset.	t_rnaedit_df
Test associations between phenotype and RNA editing levels.	TestAssociations
Transform gene symbols or region ranges into GRanges object.	TransformToGR