ChAMP 2.16.1 – Chip Analysis Methylation Pipeline for Illumina HumanMethylation450

ChAMP 2.16.1

:: DESCRIPTION

ChAMP includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number aberrations.

::DEVELOPER

Teschendorff Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
R package
BioConductor

:: DOWNLOAD

ChAMP

:: MORE INFORMATION

Citation

ChAMP: 450k Chip Analysis Methylation Pipeline.
Morris TJ, Butcher LM, Feber A, Teschendorff AE, Chakravarthy AR, Wojdacz TK, Beck S.
Bioinformatics. 2014 Feb 1;30(3):428-30. doi: 10.1093/bioinformatics/btt684.

Genome Biol. 2014 Feb 3;15(2):R30. [Epub ahead of print]
Using high-density DNA methylation arrays to profile copy number alterations.
Feber A, Guilhamon P, Lechner M, Fenton T, Wilson GA, Thirlwell C, Morris TJ, Flanagan AM, Teschendorff AE, Kelly JD, Beck S.

MethFlow 1.1 – Integral Analysis of WGBS Methylation data

MethFlow 1.1

:: DESCRIPTION

MethFlow is an optimized, open-source pipeline which performs DNA methylation profiling, detection of sequence variants, full integration with our methylation database, NGSmethDB, and differential methylation analysis.

::DEVELOPER

The group of computational genomics and bioinformatics at Granada University (Spain)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
VirtualBox.

:: DOWNLOAD

MethFlow

:: MORE INFORMATION

Citation

Ricardo Lebrón, Guillermo Barturen, Cristina Gómez, José L. Oliver, Michael Hackenberg. 2016.
MethFlow: an optimized pipeline for the integral analysis of whole-genome bisulfite sequencing methylation data (in preparation).

PCMdb – Pancreatic Cancer Methylation Database

PCMdb

:: DESCRIPTION

PCMdb is a database of methylated genes found in pancreatic cancer cell lines and tissues. In other words, it provides comprehensive information about methylation status of various genes in Pancreatic Cancer (PCa) and their comparison with transcriptomics and genomics landscape. It is a manually curated database where information is collected and compiled from literature/databases. This database will be very useful to discover novel biomakers for PCa as well as to understand the role of methylation in drug resistance.

::DEVELOPER

PCMdb team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

PCMdb: pancreatic cancer methylation database.
Nagpal G, Sharma M, Kumar S, Chaudhary K, Gupta S, Gautam A, Raghava GP.
Sci Rep. 2014 Feb 26;4:4197. doi: 10.1038/srep04197.

Bis-SNP 0.82.2 – Bisulfite Space Genotyper & Methylation Caller

BisSNP 0.82.2

:: DESCRIPTION

BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and accurate DNA methylation calling in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq, RRBS and any other bisulfite treated sequencing) with Illumina directional library protocol.

::DEVELOPER

USC Epigenome Center

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux/ Windows/MacOsX
java
perl

:: DOWNLOAD

Bis-SNP

:: MORE INFORMATION

Citation

Genome Biol. 2012 Jul 11;13(7):R61. [Epub ahead of print]
Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data.
Liu Y, Siegmund KD, Laird PW, Berman BP.