R Graphical Manual

Last data update: 2014.03.03

Data Source

R Release (3.2.3)
CranContrib
BioConductor
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Classification

Results 1 - 10 of 12 found.
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initiation_sites (Package: yCrypticRNAs) : Cryptic transcription start sites (cTSS)

For genes expresing a cryptic transcript, the method allows the identification of cTSS. Five differents methods are available.

● Data Source: CranContrib
● Keywords:
● Alias: initiation_sites
● 0 images

enrichment_score (Package: yCrypticRNAs) : 3' enrichment score

Calculates the cryptic score (3' enrichment score) using the 3'/5' ratio method as described in DeGennaro et al., 2013.

● Data Source: CranContrib
● Keywords:
● Alias: enrichment_score
● 0 images

genome_wide_scores (Package: yCrypticRNAs) : Genome-wide cryptic scores.

Genome-wide calculation of cryptic scores with a specified method.

● Data Source: CranContrib
● Keywords:
● Alias: genome_wide_scores
● 0 images

bam_to_reads (Package: yCrypticRNAs) : Convert BAM files into BED files containing the reads overlaping the specified annotations.

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

● Data Source: CranContrib
● Keywords:
● Alias: bam_to_reads
● 0 images

as.annotationsSet (Package: yCrypticRNAs) : Convert a data.table into a geneAnnotation object.

Create a geneAnnotation object containing the informations on chromosomes, start and end positions, strand, score and name of genes.

● Data Source: CranContrib
● Keywords:
● Alias: as.annotationsSet
● 0 images

coverage (Package: yCrypticRNAs) : Report coverage.

Report the coverage using bedtools coverage algorithm.

● Data Source: CranContrib
● Keywords:
● Alias: coverage
● 0 images

yCrypticRNAs (Package: yCrypticRNAs) : Cryptic transcription analysis in yeast.

This package contains functions to calculate 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.

● Data Source: CranContrib
● Keywords:
● Alias: yCrypticRNAs, yCrypticRNAs-package
● 0 images

coverageDataSet (Package: yCrypticRNAs) : Create a CoverageDataSet

Create a CoverageDataSet containing the depth and breadth of coverage of genes in annotations.

● Data Source: CranContrib
● Keywords:
● Alias: coverageDataSet
● 0 images

gene_coverage (Package: yCrypticRNAs) : Compute coverage data for a specific gene.

This function computes data for a specific gene and remove intronic regions.

● Data Source: CranContrib
● Keywords:
● Alias: gene_coverage
● 0 images

zscore_score (Package: yCrypticRNAs) : Z score

Calculates the cryptic score (z score) using the probabilistic method.

● Data Source: CranContrib
● Keywords:
● Alias: zscore_score
● 0 images