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Repitools (version 1.14.0)

Epigenomic tools

Description

Tools for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, BayMeth for quantifying methylation etc.

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Version

Version

1.14.0

License

LGPL (>= 2)

Maintainer

Mark Robinson

Last Published

February 15th, 2017

Functions in Repitools (1.14.0)

AffymetrixCelSet

Placeholder For AffymetrixCelSet Documentation

Convert an annotated GRanges to a data.frame.

A wrapper for fitting the offset-adjusted ABCD-DNA GLM

AffymetrixCdfFile

Placeholder For AffymetrixCdfFile Documentation

AdjustedCopyEstimate

Container for results of GC adjusted copy number estimation.

Convert a data.frame to a GRanges.

Calculate and Segment Absolute Copy Number from Sequencing Counts

annotationBlocksCounts

Counts the number of sequencing reads within supplied genomic blocks.

annotationBlocksLookup

Forms a mapping between probe locations and chromosomal blocks (regions).

BAM2GenomicRanges

Read in a (list of) BAM file(s) into a GRanges(List) object.

Container for results of fold change copy number estimation.

ChromaResults-class

ChromaResults class

A function to find areas of enrichment in sequencing data

Create line plots of averaged signal across a promoter

Class "BayMethList"

Visualisation of tables of feature coverages.

Positions of Genes on Human Chromosome 21

Check Probe Specificity for Some Regions

ClusteredScoresList

Container for coverage matrices with clustering results.

chromosomeCNplots

Plot copy number by chromosome

Calculate CpG Density in a Window

Boxplots of intensity, binned by Cpg Density

Function to derive regional methylation estimates.

Superfigure plots

Find occurences of a DNA pattern

Writes sequencing data out into wiggle files

Container for featureScores() output.

Calculate sequencing enrichment

Function to calculate prior parameters using empirical Bayes.

Plot Quality Checking Information for Sequencing Data

getProbePositionsDf

Translate Affymetrix probe information in a table.

makeWindowLookupTable

Using the output of 'annotationLookup', create a tabular storage of the indices

loadSampleDirectory

A routine to read Nimblegen tiling array intensities

Plot the distribution of sequencing enrichment.

Plot GC content vs. Read Counts Before Normalising, and GC content vs. Copy Estimates After Normalising.

Container for parameters for mappability and GC content adjusted absolute copy number estimation.

Vector of expression differences

mappabilityCalc

Calculate The Mappability of a Region

Plot the distribution of sequencing reads CpG densities.

MappabilitySource

Superclass for datatypes that can refer to genome mappability data.

Find Clusters Epigenetically Modified Genes

determineOffset

Function to determine the normalising offset f that accounts for the relative sequencing depth.

Calculate Absolute Copy Number from Sequencing Counts

Plot Scores of Cluster Regions

FastQC and associated classes

Plotting the response of qDNA-seq data by CNV

A container for quantitative DNA sequencing data for ABCD-DNA analyses

Find Regions of significance in microarray data

getSampleOffsets

Calculates the sample-specific offsets, using the neutral state

Make windows for distances around a reference point.

Masking files for hg19

A routine to read Nimblegen tiling array intensities

Gaussian hypergeometric function for vectorial arguments

Calculate and Segment Relative Copy Number From Sequencing Counts

Short Reads from Cancer and Normal

Create line plots of averaged signal across a promoter for gene sets, compared to random sampling.

Reads in a Nimblegen microarray design file (NDF)

summarizeScores

Subtract scores of different samples.

Set the CNVOffsets of a QdnaData object

Creates bins across a genome.

Calculate The gcContent of a Region

Function to mask suspicious regions.

mergeReplicates

Merge GRanges that are of replicate experiments.