Tag: Methylation

AgIn 0.9 – Measuring the landscape of CpG methylation of individual Repetitive Elements

AgIn 0.9

:: DESCRIPTION

AgIn (Aggregate on Intervals) processes SMRT sequencing kinetic summary to predict regional methylation on large genome.

::DEVELOPER

Morishita Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

AgIn

:: MORE INFORMATION

Citation

Suzuki Y, Korlach J, Turner SW, Tsukahara T, Taniguchi J, Qu W, Ichikawa K, Yoshimura J, Yurino H, Takahashi Y, Mitsui J, Ishiura H, Tsuji S, Takeda H, Morishita S.
AgIn: measuring the landscape of CpG methylation of individual repetitive elements.
Bioinformatics. 2016 Oct 1;32(19):2911-9. doi: 10.1093/bioinformatics/btw360. Epub 2016 Jun 17. PMID: 27318202; PMCID: PMC5039925.

MIRA – Methylation-based Inference of Regulatory Activity

MIRA

:: DESCRIPTION

The MIRA package aggregates DNA methylation across the genome for instances of a genomic feature like histone ChIP peaks, transcription factor ChIP peaks, or open chromatin regions in order to give a single signature and score for that feature, which may be used to infer regulatory activity.

::DEVELOPER

Sheffield lab of computational biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

MIRA

:: MORE INFORMATION

Citation

Lawson JT, Tomazou EM, Bock C, Sheffield NC.
MIRA: an R package for DNA methylation-based inference of regulatory activity.
Bioinformatics. 2018 Aug 1;34(15):2649-2650. doi: 10.1093/bioinformatics/bty083. PMID: 29506020; PMCID: PMC6061852.

IMA 3.1.2 – High-throughput Analysis of Illumina’s 450K Infinium Methylation data

IMA 3.1.2

:: DESCRIPTION

IMA (Illumina Methylation Analyzer) is a package designed to automate the pipeline for analyzing site-level and region-level methylation changes in epigenetic studies utilizing the 450K DNA methylation microarray.

::DEVELOPER

Dan Wang <dan.wang@roswellpark.org >

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • R

:: DOWNLOAD

 IMA

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Mar 1;28(5):729-30. doi: 10.1093/bioinformatics/bts013. Epub 2012 Jan 16.
IMA: an R package for high-throughput analysis of Illumina’s 450K Infinium methylation data.
Wang D1, Yan L, Hu Q, Sucheston LE, Higgins MJ, Ambrosone CB, Johnson CS, Smiraglia DJ, Liu S.

Methylation plotter – A Dynamic Web tool for Easy Methylation data Visualization

Methylation plotter

:: DESCRIPTION

Methylation plotter allows to generate publication-ready, high quality graphics summarizing methylation data in lollipop- and heatmap-like plots. Some descriptive stats and comparisons are provided.

::DEVELOPER

maplab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Methylation plotter: a web tool for dynamic visualization of DNA methylation data.
Mallona I, Díez-Villanueva A, Peinado MA.
Source Code Biol Med. 2014 Jun 7;9:11. doi: 10.1186/1751-0473-9-11.

CpGassoc 2.60 – Analysis of DNA Methylation Microarray data

CpGassoc 2.60

:: DESCRIPTION

CpGassoc – An R Function for Analysis of DNA Methylation Microarray Data The analysis of DNA methylation data has recently garnered attention among researchers from a variety of backgrounds, due to the availability of high-throughput methylation microarrays. The number of CpG sites that can be analyzed is growing rapidly – for example, the latest Illumina Infinium BeadChip interrogates ~450,000 CpG sites. With the growing interest in DNA methylation and the growing volume of data analyzed, there is a need for software to perform these types of analyses.

::DEVELOPER

R Barfield <barfieldrichard8 at gmail.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

CpGassoc

:: MORE INFORMATION

Citation

R. T. Barfield et al.
CpGassoc – An R Function for Analysis of DNA Methylation Microarray Data.
American Society of Human Genetics/ICHG 2011

IDEM – Identifying Direction from Expression and Methylation

IDEM

:: DESCRIPTION

IDEM is a method for identifying the causal direction of edges by combining DNA methylation and mRNA transcription data.

::DEVELOPER

David M Simcha dsimcha@gmail.com

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 IDEM

:: MORE INFORMATION

Citation

BMC Syst Biol. 2013 Nov 1;7:118. doi: 10.1186/1752-0509-7-118.
Identification of direction in gene networks from expression and methylation.
Simcha DM1, Younes L, Aryee MJ, Geman D.

Epiclomal – Clustering of sparse DNA Methylation data

Epiclomal

:: DESCRIPTION

Epiclomal package is software for clustering of sparse DNA methylation data

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

Epiclomal

:: MORE INFORMATION

Citation

Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data,
Camila P. E. de Souza, Mirela Andronescu, Tehmina Masud, Farhia Kabeer, Justina Biele, Emma Laks, Daniel Lai, Jazmine Brimhall, Beixi Wang, Edmund Su, Tony Hui, Qi Cao, Marcus Wong, Michelle Moksa, Richard A. Moore, Martin Hirst, Samuel Aparicio, Sohrab P. Shah,
doi: https://doi.org/10.1101/414482

DMAP – Differential Methylation Analysis Package

DMAP

:: DESCRIPTION

DMAP is a differential methylation analysis package to generate coverage-filtered reference methylomes and to identify differentially methylated regions across multiple samples from reduced representation bisulphite sequencing and whole genome bisulphite sequencing experiments.

::DEVELOPER

Dr Peter Stockwell, Department of Biochemistry, University of Otago

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 DMAP

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 23.
DMAP: differential methylation analysis package for RRBS and WGBS data.
Stockwell PA1, Chatterjee A, Rodger EJ, Morison IM.

InfiniumPurify 1.3.1 – Predicting Tumor Purity from Methylation Microarray data

InfiniumPurify 1.3.1

:: DESCRIPTION

InfiniumPurify is a simple but effective method to estimate purities from the DNA methylation 450k array data.

::DEVELOPER

Yufang Qin <yfqin at shou.edu.cn>

 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • R

:: DOWNLOAD

 InfiniumPurify

:: MORE INFORMATION

Citation:

Qin Y, Feng H, Chen M, Wu H, Zheng X.
InfiniumPurify: An R package for estimating and accounting for tumor purity in cancer methylation research.
Genes Dis. 2018 Feb 21;5(1):43-45. doi: 10.1016/j.gendis.2018.02.003. PMID: 30258934; PMCID: PMC6147081.

Predicting tumor purity from methylation microarray data.
Zhang N, Wu HJ, Zhang W, Wang J, Wu H, Zheng X.
Bioinformatics. 2015 Jun 25. pii: btv370.

funtooNorm 1.00.1 – Normalization of Illumina Infinium Human Methylation 450 BeadChip

funtooNorm 1.00.1

:: DESCRIPTION

The R package funtooNorm provides a function for normalization of Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K) data when there are samples from multiple tissues or cell types.

::DEVELOPER

Greenwood Lab, Statistical Genetics at the Lady Davis Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • R

:: DOWNLOAD

 funtooNorm

:: MORE INFORMATION

Citation

funtooNorm: an R package for normalization of DNA methylation data when there are multiple cell or tissue types.
Oros Klein K, Grinek S, Bernatsky S, Bouchard L, Ciampi A, Colmegna I, Fortin JP, Gao L, Hivert MF, Hudson M, Kobor MS, Labbe A, MacIsaac JL, Meaney MJ, Morin AM, O’Donnell KJ, Pastinen T, Van Ijzendoorn MH, Voisin G, Greenwood CM.
Bioinformatics. 2015 Oct 24. pii: btv615.