Package: cleanUpdTSeq 1.45.0
Jianhong Ou
cleanUpdTSeq: cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data
This package implements a Naive Bayes classifier for accurately differentiating true polyadenylation sites (pA sites) from oligo(dT)-mediated 3' end sequencing such as PAS-Seq, PolyA-Seq and RNA-Seq by filtering out false polyadenylation sites, mainly due to oligo(dT)-mediated internal priming during reverse transcription. The classifer is highly accurate and outperforms other heuristic methods.
Authors:
cleanUpdTSeq_1.45.0.tar.gz
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cleanUpdTSeq.pdf |cleanUpdTSeq.html✨
cleanUpdTSeq/json (API)
NEWS
| # Install 'cleanUpdTSeq' in R: |
| install.packages('cleanUpdTSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- classifier - NaiveBayes classifier
- data.NaiveBayes - Training Data
On BioConductor:cleanUpdTSeq-1.45.0(bioc 3.21)cleanUpdTSeq-1.44.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
sequencing3 end sequencingpolyadenylation siteinternal priming
Last updated 2 months agofrom:0239c1be22. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | OK | Nov 29 2024 |
| R-4.5-linux | OK | 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:BED6WithSeq2GRangesSeqbuildClassifierbuildFeatureVectorgetContextSequencespredictTestSet
Dependencies:abindade4askpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomeBSgenome.Drerio.UCSC.danRer7classclicodetoolscpp11crayoncurlDelayedArraye1071formatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmimenlmeopensslpixmapproxyR6RcppRcppArmadilloRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorssegmentedseqinrsnowspSparseArraystringistringrSummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Covert (extended) BED6 file to a GRanges object | BED6WithSeq2GRangesSeq |
| Build a Naive Bayes Classifier | buildClassifier |
| build Feature Vector_2 | buildFeatureVector |
| NaiveBayes classifier | classifier |
| This package classifies putative polyadenylation sites. | cleanUpdTSeq-package cleanUpdTSeq |
| Training Data | data.NaiveBayes |
| Class '"featureVector"' | $,featureVector-method $<-,featureVector-method featureVector featureVector-class |
| Retrieve upstream and downstream sequences | getContextSequences |
| Class '"modelInfo"' | $,modelInfo-method $<-,modelInfo-method modelInfo modelInfo-class |
| Class '"naiveBayes"' | $,naiveBayes-method $<-,naiveBayes-method naiveBayes naiveBayes-class |
| Class '"PASclassifier"' | $,PASclassifier-method $<-,PASclassifier-method PASclassifier PASclassifier-class |
| predict authenticity of putative pA sites | predictTestSet |
