Package: atena 1.19.0
Robert Castelo
atena: Analysis of Transposable Elements
Quantify expression of transposable elements (TEs) from RNA-seq data through different methods, including ERVmap, TEtranscripts and Telescope. A common interface is provided to use each of these methods, which consists of building a parameter object, calling the quantification function with this object and getting a SummarizedExperiment object as output container of the quantified expression profiles. The implementation allows one to quantify TEs and gene transcripts in an integrated manner.
Authors:
atena_1.19.0.tar.gz
atena_1.19.0.zip(r-4.7)atena_1.19.0.zip(r-4.6)atena_1.19.0.zip(r-4.5)
atena_1.19.0.tgz(r-4.6-any)atena_1.19.0.tgz(r-4.5-any)
atena_1.19.0.tar.gz(r-4.7-any)atena_1.19.0.tar.gz(r-4.6-any)
atena_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
atena/json (API)
NEWS
| # Install 'atena' in R: |
| install.packages('atena', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rcastelo/atena/issues
On BioConductor:atena-1.19.0(bioc 3.24)atena-1.18.0(bioc 3.23)
transcriptiontranscriptomicsrnaseqsequencingpreprocessingsoftwaregeneexpressioncoveragedifferentialexpressionfunctionalgenomics
Last updated from:4524201929. Checks:1 NOTE, 7 WARNING, 1 ERROR, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 218 | ||
| linux-devel-x86_64 | WARNING | 482 | ||
| source / vignettes | ERROR | 388 | ||
| linux-release-x86_64 | WARNING | 518 | ||
| macos-release-arm64 | WARNING | 344 | ||
| macos-oldrel-arm64 | WARNING | 327 | ||
| windows-devel | WARNING | 441 | ||
| windows-release | WARNING | 411 | ||
| windows-oldrel | WARNING | 417 | ||
| wasm-release | OK | 183 |
Exports:annotaTEsatenaParamERVmapParamfeaturesgetDNAtransposonsgetLINEsgetLTRsgetSINEsOneCodeToFindThemAllovIntersectionStrictovUnionpathqtexrmskatenaparserrmskbasicparserrmskidentityshowTelescopeParamTEtranscriptsParam
Dependencies:abindAnnotationDbiAnnotationHubaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydplyrfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrhttr2IRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpurrrR6rappdirsRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraysparseMatrixStatsSQUAREMstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| atena: analysis of transposable elements in R and Bioconductor | atena-package atena |
| Get RepeatMasker UCSC annotations | annotaTEs |
| Getter functions of TE classes from parsed RepeatMasker annotations. | annotateTEsGetters getDNAtransposons getLINEs getLTRs getSINEs |
| atena parameter class | atenaParam atenaParam-class show,atenaParam-method |
| ERVmap parameter class | ERVmapParam ERVmapParam-class show,ERVmapParam-method |
| OneCodeToFindThemAll parser of RepeatMasker annotations | OneCodeToFindThemAll |
| Pre-defined overlapping mode functions | ovIntersectionStrict ovUnion |
| Quantify transposable element expression | qtex qtex,AtenaParam-method qtex,atenaParam-method qtex,ERVmapParam-method qtex,TelescopeParam-method qtex,TEtranscriptsParam-method |
| QuantifyParam parameter class | features,QuantifyParam-method path,QuantifyParam-method QuantifyParam-class |
| atena annotation parser of RepeatMasker annotations | rmskatenaparser |
| Parser of RepeatMasker annotations | rmskbasicparser |
| Identity function for parsefun | rmskidentity |
| Telescope parameter class | show,TelescopeParam-method TelescopeParam TelescopeParam-class |
| TEtranscripts parameter class | show,TEtranscriptsParam-method TEtranscriptsParam TEtranscriptsParam-class |
