cleanUpdTSeq: This package classifies putative polyadenylation sites as true or false/internally oligodT primed

This package uses the Naive Bayes classifier (from e1071) to assign probability values to putative polyadenylation sites (pA sites) based on training data from zebrafish. This will allow the user to separate true, biologically relevant pA sites from false, oligodT primed pA sites.

AuthorSarah Sheppard, Jianhong Ou, Nathan Lawson, Lihua Julie Zhu
Date of publicationNone
MaintainerSarah Sheppard <Sarah.Sheppard@umassmed.edu>; Jianhong Ou <Jianhong.Ou@umassmed.edu>; Lihua Julie Zhu <Julie.Zhu@umassmed.edu>
LicenseGPL-2
Version1.12.0

View on Bioconductor

Files

cleanUpdTSeq/DESCRIPTION
cleanUpdTSeq/NAMESPACE
cleanUpdTSeq/NEWS
cleanUpdTSeq/R
cleanUpdTSeq/R/AllClasses.R cleanUpdTSeq/R/BED2GRangesSeq.R cleanUpdTSeq/R/buildClassifier.R cleanUpdTSeq/R/buildFeatureVector.R cleanUpdTSeq/R/getDownstreamSequence.R cleanUpdTSeq/R/getUpstreamSequence.R cleanUpdTSeq/R/predictTestSet.R
cleanUpdTSeq/build
cleanUpdTSeq/build/vignette.rds
cleanUpdTSeq/data
cleanUpdTSeq/data/classifier.rda
cleanUpdTSeq/data/data.NaiveBayes.rda
cleanUpdTSeq/data/datalist
cleanUpdTSeq/inst
cleanUpdTSeq/inst/CITATION
cleanUpdTSeq/inst/doc
cleanUpdTSeq/inst/doc/cleanUpdTSeq.R
cleanUpdTSeq/inst/doc/cleanUpdTSeq.Rmd
cleanUpdTSeq/inst/doc/cleanUpdTSeq.html
cleanUpdTSeq/inst/extdata
cleanUpdTSeq/inst/extdata/test-predNaiveBayes.rds
cleanUpdTSeq/inst/extdata/test-predNaiveBayes.xls
cleanUpdTSeq/inst/extdata/test.bed
cleanUpdTSeq/inst/unitTests
cleanUpdTSeq/inst/unitTests/test_predictTestSet.R
cleanUpdTSeq/man
cleanUpdTSeq/man/BED2GRangesSeq.Rd cleanUpdTSeq/man/PASclassifier-class.Rd cleanUpdTSeq/man/buildClassifier.Rd cleanUpdTSeq/man/buildFeatureVector.Rd cleanUpdTSeq/man/classifier.Rd cleanUpdTSeq/man/cleanUpdTSeq-package.Rd cleanUpdTSeq/man/data.NaiveBayes.Rd cleanUpdTSeq/man/featureVector-class.Rd cleanUpdTSeq/man/getDownstreamSequence.Rd cleanUpdTSeq/man/getUpstreamSequence.Rd cleanUpdTSeq/man/modelInfo-class.Rd cleanUpdTSeq/man/naiveBayes.Rd cleanUpdTSeq/man/predictTestSet.Rd
cleanUpdTSeq/tests
cleanUpdTSeq/tests/runTests.R
cleanUpdTSeq/vignettes
cleanUpdTSeq/vignettes/cleanUpdTSeq.Rmd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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