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).

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

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

  NO

:: 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.

methylFlow – Cell-specific Methylation Pattern Reconstruction

methylFlow

:: DESCRIPTION

methylFlow is a software of cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing.

::DEVELOPER

HCBravo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 methylFlow

:: MORE INFORMATION

Citation

methylFlow: cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing.
Dorri F, Mendelowitz L, Corrada Bravo H.
Bioinformatics. 2016 Jun 1;32(11):1618-24. doi: 10.1093/bioinformatics/btw287

Methpat 2.0.0 – A program for Summarising CpG Methylation Patterns

Methpat 2.0.0

:: DESCRIPTION

Methpat summarises the resultant DNA methylation pattern data from the output of Bismark bismark_methylation_extractor.

::DEVELOPER

Bernie Pope

: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Python
  • Bismark v0.12.2 and it’s dependencies (bwa v0.7.5a-r405).

:: DOWNLOAD

 Methpat

:: MORE INFORMATION

Citation

MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing.
Wong NC, Pope BJ, Candiloro IL, Korbie D, Trau M, Wong SQ, Mikeska T, Zhang X, Pitman M, Eggers S, Doyle SR, Dobrovic A.
BMC Bioinformatics. 2016 Feb 24;17(1):98. doi: 10.1186/s12859-016-0950-8.

SRAMP – Sequence-based RNA Adenosine Methylation Site Predictor

SRAMP

:: DESCRIPTION

SRAMP would serve as a useful tool to predict m6A modification sites on the RNA sequences

::DEVELOPER

the Cui Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

SRAMP: prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features.
Zhou Y, Zeng P, Li YH, Zhang Z, Cui Q.
Nucleic Acids Res. 2016 Feb 20. pii: gkw104.

DRME – Differential RNA Methylation Analysis

DRME

:: DESCRIPTION

DRME is an R package of count-based differential RNA methylation analysis at small sample size scenario.

::DEVELOPER

DRME team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • R

:: DOWNLOAD

 DRME

:: MORE INFORMATION

Citation

DRME: Count-based differential RNA methylation analysis at small sample size scenario.
Liu L, Zhang SW, Gao F, Zhang Y, Huang Y, Chen R, Meng J.
Anal Biochem. 2016 Feb 4;499:15-23. doi: 10.1016/j.ab.2016.01.014

funtooNorm 0.99.1 – Normalization of Illumina Infinium Human Methylation 450 BeadChip

funtooNorm 0.99.1

:: 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.

ChAMP 1.6.2 – Chip Analysis Methylation Pipeline for Illumina HumanMethylation450

ChAMP 1.6.2

:: 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

Tiffany Morris, PhD  <Tiffany.Morris at ucl.ac.uk>

:: 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.

BSHMM – DNA Methylation Analysis, based on hidden Markov models

BSHMM

:: DESCRIPTION

BSHMM is a software of methylation profile analysis using hidden Markov models.

::DEVELOPER

Laboratory of Computational and Quantitative Biology(LCQB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BSHMM

:: MORE INFORMATION