yCrypticRNAs: Cryptic Transcription Analysis in Yeast

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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.

Author
Nicole Uwimana, Benjamin Haibe-Kains, Francois Robert
Date of publication
2016-02-08 23:43:06
Maintainer
Nicole Uwimana <nicole.uwimana@gmail.com>
License
GPL-2
Version
0.99.2
URLs

View on CRAN

Man pages

annotations
Saccharomyce cerevisiae genes annotations.
annotationsSet
Create a geneAnnotation object.
as.annotationsSet
Convert a data.table into a geneAnnotation object.
bam_to_reads
Convert BAM files into BED files containing the reads...
coverage
Report coverage.
coverageDataSet
Create a CoverageDataSet
enrichment_score
3' enrichment score
gene_coverage
Compute coverage data for a specific gene.
genome_wide_scores
Genome-wide cryptic scores.
initiation_sites
Cryptic transcription start sites (cTSS)
introns
Saccharomyce cerevisiae introns annotations.
ratio_score
3'/5' ratio score
rna_seq_signals
Coverage dataset for FLO8, CDC14 and SNC1 gene.
yCrypticRNAs
Cryptic transcription analysis in yeast.
yer109c
Coverage dataset for FLO8 gene.
zscore_score
Z score

Files in this package

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