Package: raer 1.10.0

Kent Riemondy

raer: RNA editing tools in R

Toolkit for identification and statistical testing of RNA editing signals from within R. Provides support for identifying sites from bulk-RNA and single cell RNA-seq datasets, and general methods for extraction of allelic read counts from alignment files. Facilitates annotation and exploratory analysis of editing signals using Bioconductor packages and resources.

Authors:Kent Riemondy [aut, cre], Kristen Wells-Wrasman [aut], Ryan Sheridan [ctb], Jay Hesselberth [ctb], RNA Bioscience Initiative [cph, fnd]

raer_1.10.0.tar.gz
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raer_1.10.0.tgz(r-4.6-x86_64)raer_1.10.0.tgz(r-4.6-arm64)raer_1.10.0.tgz(r-4.5-x86_64)raer_1.10.0.tgz(r-4.5-arm64)
raer_1.10.0.tar.gz(r-4.7-arm64)raer_1.10.0.tar.gz(r-4.7-x86_64)raer_1.10.0.tar.gz(r-4.6-arm64)raer_1.10.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
raer/json (API)
NEWS

# Install 'raer' in R:
install.packages('raer', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rnabioco/raer/issues

Pkgdown/docs site:https://rnabioco.github.io

Uses libs:
  • curl– Easy-to-use client-side URL transfer library
  • bzip2– High-quality block-sorting file compressor library
  • xz-utils– XZ-format compression library
  • zlib– Compression library

On BioConductor:raer-1.11.0(bioc 3.24)raer-1.10.0(bioc 3.23)

multiplecomparisonrnaseqsinglecellsequencingcoverageepitranscriptomicsfeatureextractionannotationalignmentbioconductor-packagerna-seq-analysissingle-cell-analysissingle-cell-rna-seqcurlbzip2xz-utilszlib

4.78 score 10 stars 7 scripts 334 downloads 23 exports 70 dependencies

Last updated from:016a9f4445 (on RELEASE_3_23). Checks:1 NOTE, 11 WARNING, 1 ERROR, 1 FAIL. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE449
linux-devel-arm64WARNING574
linux-devel-x86_64WARNING708
source / vignettesERROR715
linux-release-arm64WARNING624
linux-release-x86_64WARNING680
macos-release-arm64WARNING583
macos-release-x86_64WARNING1075
macos-oldrel-arm64WARNING414
macos-oldrel-x86_64WARNING851
windows-develWARNING690
windows-releaseWARNING563
windows-oldrelWARNING658
wasm-releaseFAIL369

Exports:annot_from_grannot_snpscalc_AEIcalc_confidencecalc_edit_frequencycalc_scAEIcorrect_strandfilter_clustered_variantsfilter_multiallelicfilter_splice_variantsFilterParamfind_de_sitesfind_mispriming_sitesfind_scde_sitesget_overlapping_snpsget_scAEI_sitesget_splice_sitesmake_de_objectmock_rsepileup_cellspileup_sitesraer_exampleread_sparray

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfoSingleCellExperimentsnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryaml