Package: raer 1.3.0

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_1.3.0.tar.gz
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raer.pdf |raer.html✨
raer/json (API)
NEWS

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

Peer review:

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

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-1.3.0(bioc 3.20)raer-1.2.0(bioc 3.19)

bioconductor-package

23 exports 1.90 score 70 dependencies

Last updated 2 months agofrom:27290f632a

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:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSingleCellExperimentsnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryamlzlibbioc

Introducing the raer package

Kent Riemondy, Kristen Wells-Wrasman, Jay Hesselberth

Rendered fromraer.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2024-03-13
Started: 2022-05-02