R-universe search: topic:cpgisland

Showing 12 of total 12 results (show query)

bioc

genomation:Summary, annotation and visualization of genomic data

A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.

Maintained by Altuna Akalin. Last updated 5 months ago.

annotation sequencing visualization cpgisland cpp

76 stars 11.13 score 738 scripts 5 dependents

bioc

methylumi:Handle Illumina methylation data

This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.

Maintained by Sean Davis. Last updated 5 months ago.

dnamethylation twochannel preprocessing qualitycontrol cpgisland

9 stars 9.90 score 89 scripts 9 dependents

bioc

RnBeads:RnBeads

RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.

Maintained by Fabian Mueller. Last updated 2 months ago.

dnamethylation methylationarray methylseq epigenetics qualitycontrol preprocessing batcheffect differentialmethylation sequencing cpgisland immunooncology twochannel dataimport

6.85 score 169 scripts 1 dependents

bioc

planet:Placental DNA methylation analysis tools

This package contains R functions to predict biological variables to from placnetal DNA methylation data generated from infinium arrays. This includes inferring ethnicity/ancestry, gestational age, and cell composition from placental DNA methylation array (450k/850k) data.

Maintained by Victor Yuan. Last updated 2 months ago.

software differentialmethylation epigenetics microarray methylationarray dnamethylation cpgisland ancestry dna-methylation-data genetics inference machine-learning placenta

4 stars 5.64 score 12 scripts 1 dependents

bioc

bigmelon:Illumina methylation array analysis for large experiments

Methods for working with Illumina arrays using gdsfmt.

Maintained by Leonard C. Schalkwyk. Last updated 5 months ago.

dnamethylation microarray twochannel preprocessing qualitycontrol methylationarray dataimport cpgisland

5.47 score 21 scripts

bioc

HELP:Tools for HELP data analysis

The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications.

Maintained by Reid F. Thompson. Last updated 5 months ago.

cpgisland dnamethylation microarray twochannel dataimport qualitycontrol preprocessing visualization

5.18 score 76 scripts

bioc

MEDIPS:DNA IP-seq data analysis

MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, MEDIPS provides functionalities for the analysis of any kind of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential coverage between groups of samples and saturation and correlation analysis.

Maintained by Lukas Chavez. Last updated 5 months ago.

dnamethylation cpgisland differentialexpression sequencing chipseq preprocessing qualitycontrol visualization microarray genetics coverage genomeannotation copynumbervariation sequencematching

5.17 score 74 scripts

bioc

MAGAR:MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

"Methylation-Aware Genotype Association in R" (MAGAR) computes methQTL from DNA methylation and genotyping data from matched samples. MAGAR uses a linear modeling stragety to call CpGs/SNPs that are methQTLs. MAGAR accounts for the local correlation structure of CpGs.

Maintained by Michael Scherer. Last updated 5 months ago.

regression epigenetics dnamethylation snp geneticvariability methylationarray microarray cpgisland methylseq sequencing mrnamicroarray preprocessing copynumbervariation twochannel immunooncology differentialmethylation batcheffect qualitycontrol dataimport network clustering graphandnetwork

4.30 score 3 scripts

bioc

PoDCall:Positive Droplet Calling for DNA Methylation Droplet Digital PCR

Reads files exported from 'QX Manager or QuantaSoft' containing amplitude values from a run of ddPCR (96 well plate) and robustly sets thresholds to determine positive droplets for each channel of each individual well. Concentration and normalized concentration in addition to other metrics is then calculated for each well. Results are returned as a table, optionally written to file, as well as optional plots (scatterplot and histogram) for both channels per well written to file. The package includes a shiny application which provides an interactive and user-friendly interface to the full functionality of PoDCall.

Maintained by Hans Petter Brodal. Last updated 2 months ago.

classification epigenetics ddpcr differentialmethylation cpgisland dnamethylation

4.30 score 5 scripts

bioc

MEDME:Modelling Experimental Data from MeDIP Enrichment

MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments

Maintained by Mattia Pelizzola. Last updated 5 months ago.

microarray cpgisland dnamethylation

4.30 score 2 scripts

bioc

TurboNorm:A fast scatterplot smoother suitable for microarray normalization

A fast scatterplot smoother based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available.

Maintained by Maarten van Iterson. Last updated 5 months ago.

microarray onechannel twochannel preprocessing dnamethylation cpgisland methylationarray normalization

3.30 score 1 scripts

bioc

qsea:IP-seq data analysis and vizualization

qsea (quantitative sequencing enrichment analysis) was developed as the successor of the MEDIPS package for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, qsea provides several functionalities for the analysis of other kinds of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential enrichment between groups of samples.

Maintained by Matthias Lienhard. Last updated 5 months ago.

sequencing dnamethylation cpgisland chipseq preprocessing normalization qualitycontrol visualization copynumbervariation chiponchip differentialmethylation

3.30 score 7 scripts