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.

Install the latest version of this package by entering the following in R:
install.packages("yCrypticRNAs")
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

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

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

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