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Repitools (version 1.18.0)

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

1.18.0

License

LGPL (>= 2)

Maintainer

Mark Robinson

Last Published

February 15th, 2017

Functions in Repitools (1.18.0)

ChromaResults-class

ChromaResults class

Plot Quality Checking Information for Sequencing Data

mappabilityCalc

Calculate The Mappability of a Region

BAM2GenomicRanges

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

Set the CNVOffsets of a QdnaData object

AffymetrixCdfFile

Placeholder For AffymetrixCdfFile Documentation

Boxplots of intensity, binned by Cpg Density

Make windows for distances around a reference point.

Get scores at regular sample points around genomic features.

Calculate Absolute Copy Number from Sequencing Counts

Plot Scores of Cluster Regions

Container for results of fold change copy number estimation.

Create line plots of averaged signal across a promoter

Positions of Genes on Human Chromosome 21

AdjustedCopyEstimate

Container for results of GC adjusted copy number estimation.

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

annotationCounts

Counts the number of sequencing reads surrounding supplied annotations

Visualisation of tables of feature coverages.

chromosomeCNplots

Plot copy number by chromosome

Plot the distribution of sequencing reads CpG densities.

Function to derive regional methylation estimates.

Masking files for hg19

getProbePositionsDf

Translate Affymetrix probe information in a table.

mergeReplicates

Merge GRanges that are of replicate experiments.

makeWindowLookupTable

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

Gaussian hypergeometric function for vectorial arguments

Plotting the response of qDNA-seq data by CNV

Reads in a Nimblegen microarray design file (NDF)

Container for featureScores() output.

Calculate and Segment Absolute Copy Number from Sequencing Counts

Vector of expression differences

Find occurences of a DNA pattern

Check Probe Specificity for Some Regions

Function to mask suspicious regions.

ClusteredScoresList

Container for coverage matrices with clustering results.

Calculate and Segment Relative Copy Number From Sequencing Counts

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

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

A function to find areas of enrichment in sequencing data

Writes sequencing data out into wiggle files

Function to calculate prior parameters using empirical Bayes.

Convert an annotated GRanges to a data.frame.

Calculate The gcContent of a Region

Superfigure plots

AffymetrixCelSet

Placeholder For AffymetrixCelSet Documentation

annotationBlocksCounts

Counts the number of sequencing reads within supplied genomic blocks.

Creates bins across a genome.

getSampleOffsets

Calculates the sample-specific offsets, using the neutral state

MappabilitySource

Superclass for datatypes that can refer to genome mappability data.

annotationLookup

Forms a mapping between probes on a tiling array and windows surrounding the TSSs of genes.

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

determineOffset

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

Calculate sequencing enrichment

Plot the distribution of sequencing enrichment.

Convert a data.frame to a GRanges.

loadSampleDirectory

A routine to read Nimblegen tiling array intensities

Class "BayMethList"

FastQC and associated classes

A routine to read Nimblegen tiling array intensities

annotationBlocksLookup

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

Calculate statistics for regions in the genome

Calculate CpG Density in a Window

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

Find Clusters Epigenetically Modified Genes

Short Reads from Cancer and Normal

Find Regions of significance in microarray data

summarizeScores

Subtract scores of different samples.