Tag: WGBS

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).

bsmooth-align 0.8.1 – Analyzing Whole Genome Bisulfite Sequencing (WGBS) data

bsmooth-align

:: DESCRIPTION

bsmooth-align (version 0.8.1). This integrates two different pipelines for aligning WGBS data.

bsseq. This is a R package used for smoothing methylation profiles and identifying DMRs.

bsseqData This is an experiment data package for R, containing an example dataset used in the vignettes (chromosome 21 and 22 from 3 normal colon and 3 colon cancer patients).

::DEVELOPER

RafaLab, Hansen Lab

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioCOnductor

:: DOWNLOAD

 bsmooth-align, bsseq ,bsseqData

:: MORE INFORMATION

Citation

Genome Biol. 2012 Oct 3;13(10):R83.
BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.
Hansen KD1, Langmead B, Irizarry RA.