# Cryptic Transcription Analysis in Yeast

## Documentation for package ‘yCrypticRNAs’ version 0.99.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

yCrypticRNAs-package | Cryptic transcription analysis in yeast.
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 overlaping the specified annotations.
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