Package: raer 1.5.0

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_1.5.0.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'))

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

Pkgdown 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-1.5.0(bioc 3.21)raer-1.4.0(bioc 3.20)

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

5.98 score 8 stars 6 scripts 144 downloads 23 exports 70 dependencies

Last updated 4 months agofrom:438c2455de. Checks:1 OK, 10 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 29 2025
R-4.5-win-x86_64NOTEJan 29 2025
R-4.5-mac-x86_64NOTEJan 29 2025
R-4.5-mac-aarch64NOTEJan 29 2025
R-4.5-linux-x86_64NOTEJan 29 2025
R-4.4-win-x86_64NOTEJan 29 2025
R-4.4-mac-x86_64NOTEJan 29 2025
R-4.4-mac-aarch64NOTEJan 29 2025
R-4.3-win-x86_64NOTEJan 29 2025
R-4.3-mac-x86_64NOTEJan 29 2025
R-4.3-mac-aarch64NOTEJan 29 2025

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.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSingleCellExperimentsnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryaml

Introducing the raer package

Kent Riemondy, Kristen Wells-Wrasman, Jay Hesselberth

Rendered fromraer.Rmdusingknitr::rmarkdownon Jan 29 2025.

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