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yCrypticRNAs (version 0.99.2)

Cryptic Transcription Analysis in Yeast

Description

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.

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Version

Install

install.packages('yCrypticRNAs')

Monthly Downloads

24

Version

0.99.2

License

GPL-2

Maintainer

Nicole Uwimana

Last Published

February 8th, 2016

Functions in yCrypticRNAs (0.99.2)

gene_coverage

Compute coverage data for a specific gene.
coverageDataSet

Create a CoverageDataSet
as.annotationsSet

Convert a data.table into a geneAnnotation object.
initiation_sites

Cryptic transcription start sites (cTSS)
coverage

Report coverage.
yCrypticRNAs

Cryptic transcription analysis in yeast.
annotations

Saccharomyce cerevisiae genes annotations.
annotationsSet

Create a geneAnnotation object.
rna_seq_signals

Coverage dataset for FLO8, CDC14 and SNC1 gene.
yer109c

Coverage dataset for FLO8 gene.
introns

Saccharomyce cerevisiae introns annotations.
ratio_score

3'/5' ratio score
zscore_score

Z score
enrichment_score

3' enrichment score
genome_wide_scores

Genome-wide cryptic scores.
bam_to_reads

Convert BAM files into BED files containing the reads overlaping the specified annotations.