yCrypticRNAs: Cryptic Transcription Analysis in Yeast

Calculates cryptic scores for genes using the ratio (Cheung et al., 2008), the 3' enrichment method (DeGennaro et al., 2013) and the probabilistic method. It also provide methods to estimates cryptic transcription start sites.

AuthorNicole Uwimana, Benjamin Haibe-Kains, Francois Robert
Date of publication2016-02-08 23:43:06
MaintainerNicole Uwimana <nicole.uwimana@gmail.com>
LicenseGPL-2
Version0.99.2
https://bitbucket.org/nuwimana/ycrypticrnas

View on CRAN

Files

yCrypticRNAs
yCrypticRNAs/inst
yCrypticRNAs/inst/extdata
yCrypticRNAs/inst/extdata/mut_rep2.bam
yCrypticRNAs/inst/extdata/mut_rep1.bam
yCrypticRNAs/inst/extdata/wt_rep2.bam
yCrypticRNAs/inst/extdata/wt_rep1.bam
yCrypticRNAs/inst/doc
yCrypticRNAs/inst/doc/yCrypticRNAs.pdf
yCrypticRNAs/inst/doc/yCrypticRNAs.R
yCrypticRNAs/inst/doc/yCrypticRNAs.Rmd
yCrypticRNAs/tests
yCrypticRNAs/tests/yCrypticRNAs_tests.R
yCrypticRNAs/tests/testthat.R
yCrypticRNAs/tests/testthat
yCrypticRNAs/tests/testthat/test-string.R
yCrypticRNAs/src
yCrypticRNAs/src/my_coverage.h
yCrypticRNAs/src/bedFile.h
yCrypticRNAs/src/bedFile.cpp
yCrypticRNAs/src/lineFileUtilities.h
yCrypticRNAs/src/BlockedIntervals.cpp
yCrypticRNAs/src/my_coverage.cpp
yCrypticRNAs/src/my_coverageMain.cpp
yCrypticRNAs/src/RcppExports.cpp
yCrypticRNAs/src/BlockedIntervals.h
yCrypticRNAs/NAMESPACE
yCrypticRNAs/data
yCrypticRNAs/data/annotations.rda
yCrypticRNAs/data/rna_seq_signals.rda
yCrypticRNAs/data/yer109c.rda
yCrypticRNAs/data/introns.rda
yCrypticRNAs/R
yCrypticRNAs/R/utils.R yCrypticRNAs/R/coverageDataSet.R yCrypticRNAs/R/datasets-documentations.R yCrypticRNAs/R/cryptic_transcripts_methods.R yCrypticRNAs/R/annotationSet.R yCrypticRNAs/R/RcppExports.R yCrypticRNAs/R/yCrypticRNAs.R yCrypticRNAs/R/initiation_points_methods.R
yCrypticRNAs/vignettes
yCrypticRNAs/vignettes/yCrypticRNAs.Rmd
yCrypticRNAs/MD5
yCrypticRNAs/build
yCrypticRNAs/build/vignette.rds
yCrypticRNAs/DESCRIPTION
yCrypticRNAs/man
yCrypticRNAs/man/rna_seq_signals.Rd yCrypticRNAs/man/initiation_sites.Rd yCrypticRNAs/man/introns.Rd yCrypticRNAs/man/enrichment_score.Rd yCrypticRNAs/man/genome_wide_scores.Rd yCrypticRNAs/man/bam_to_reads.Rd yCrypticRNAs/man/as.annotationsSet.Rd yCrypticRNAs/man/yer109c.Rd yCrypticRNAs/man/coverage.Rd yCrypticRNAs/man/yCrypticRNAs.Rd yCrypticRNAs/man/annotations.Rd yCrypticRNAs/man/coverageDataSet.Rd yCrypticRNAs/man/gene_coverage.Rd yCrypticRNAs/man/zscore_score.Rd yCrypticRNAs/man/annotationsSet.Rd yCrypticRNAs/man/ratio_score.Rd

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