Package: atena 1.13.0
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:
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atena.pdf |atena.html✨
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-1.13.0(bioc 3.21)atena-1.12.0(bioc 3.20)
transcriptiontranscriptomicsrnaseqsequencingpreprocessingsoftwaregeneexpressioncoveragedifferentialexpressionfunctionalgenomics
Last updated 2 months agofrom:0778c4ed39. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | OK | Nov 29 2024 |
| R-4.4-mac | OK | Nov 29 2024 |
| R-4.3-win | OK | Nov 29 2024 |
| R-4.3-mac | OK | Nov 29 2024 |
Exports:annotaTEsatenaParamERVmapParamfeaturesgetDNAtransposonsgetLINEsgetLTRsgetSINEsOneCodeToFindThemAllovIntersectionStrictovUnionpathqtexrmskatenaparserrmskbasicparserrmskidentityshowTelescopeParamTEtranscriptsParam
Dependencies:abindAnnotationDbiAnnotationHubaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydplyrfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngpurrrR6rappdirsRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraysparseMatrixStatsSQUAREMstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXMLXVectoryamlzlibbioc
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 |
