Introduction | Citation | step-by-step guide | Step 1. Load the cleanUpdTSeq package, and then use the function BED6WithSeq2GRangesSeq to convert the test dataset in a extended BED6 file to a GRanges object with or without sequence information. | Step2. Build feature vectors for the classifier using the function buildFeatureVector. | Step 3. Load the training dataset and classify putative polyadenylation sites. | References | Session Info
Package: cleanUpdTSeq 1.51.0
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_1.51.0.tar.gz
cleanUpdTSeq_1.51.0.zip(r-4.7)cleanUpdTSeq_1.51.0.zip(r-4.6)cleanUpdTSeq_1.51.0.zip(r-4.5)
cleanUpdTSeq_1.51.0.tgz(r-4.6-any)cleanUpdTSeq_1.51.0.tgz(r-4.5-any)
cleanUpdTSeq_1.51.0.tar.gz(r-4.7-any)cleanUpdTSeq_1.51.0.tar.gz(r-4.6-any)
cleanUpdTSeq_1.51.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cleanUpdTSeq/json (API)
| # Install 'cleanUpdTSeq' in R: |
| install.packages('cleanUpdTSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- classifier - NaiveBayes classifier
- data.NaiveBayes - Training Data
On BioConductor:cleanUpdTSeq-1.51.0(bioc 3.24)cleanUpdTSeq-1.50.0(bioc 3.23)
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 from:4d5f8756ee. Checks:1 ERROR, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 245 | ||
| linux-devel-x86_64 | OK | 440 | ||
| source / vignettes | OK | 378 | ||
| linux-release-x86_64 | OK | 355 | ||
| macos-release-arm64 | OK | 275 | ||
| macos-oldrel-arm64 | OK | 272 | ||
| windows-devel | OK | 348 | ||
| windows-release | OK | 387 | ||
| windows-oldrel | OK | 359 | ||
| wasm-release | OK | 195 |
Exports:BED6WithSeq2GRangesSeqbuildClassifierbuildFeatureVectorgetContextSequencespredictTestSet
Dependencies:abindade4askpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomeBSgenome.Drerio.UCSC.danRer7cigarilloclassclicodetoolscpp11crayoncurlDelayedArraye1071formatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmimenlmeopensslpixmapproxyR6RcppRcppArmadilloRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorssegmentedSeqinfoseqinrsnowspSparseArraystringistringrSummarizedExperimentsysvctrsXMLXVectoryaml
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 |