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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
Version
0.99.2
0.99.1
0.99.0
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Install
install.packages('yCrypticRNAs')
Monthly Downloads
33
Version
0.99.2
License
GPL-2
Maintainer
Nicole Uwimana
Last Published
February 8th, 2016
Functions in yCrypticRNAs (0.99.2)
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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.