:: DESCRIPTION
DRME is an R package of count-based differential RNA methylation analysis at small sample size scenario.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: 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
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SRAMP would serve as a useful tool to predict m6A modification sites on the RNA sequences
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
RADAR is a comprehensive analytical tool for detecting differentially methylated loci in MeRIP-seq data.
::DEVELOPER
Chen Group at U Chicago
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhang Z, Zhan Q, Eckert M, Zhu A, Chryplewicz A, De Jesus DF, Ren D, Kulkarni RN, Lengyel E, He C, Chen M.
RADAR: differential analysis of MeRIP-seq data with a random effect model.
Genome Biol. 2019 Dec 23;20(1):294. doi: 10.1186/s13059-019-1915-9. PMID: 31870409; PMCID: PMC6927177.
:: DESCRIPTION
CNAmet is an algorithm and R package that facilitates the integration of copy number, methylation and expression data. In addition to the CNAmet algorithm, the R package includes the S2N algorithm for the integration of copy number to expression data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
CNAmet: an R package for integrating copy number, methylation and expression data
Riku Louhimo and Sampsa Hautaniemi
Bioinformatics (2011) 27 (6): 887-888.
:: DESCRIPTION
SeSAMe is an R package for processing Infinium DNA methylation data. SeSAMe currently supports EPIC, HM450 and HM27 platforms and dynamically generated manifest.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhou W, Triche TJ Jr, Laird PW, Shen H.
SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions.
Nucleic Acids Res. 2018 Nov 16;46(20):e123. doi: 10.1093/nar/gky691. PMID: 30085201; PMCID: PMC6237738.
:: DESCRIPTION
methylFlow is a software of cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: DESCRIPTION
FadE is a software package which was designed to determine the methylation parameter at each cytosine or cytosine-guanine position in the human genome. FadE uses color reads produced by the SOLiD sequencer.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2013 Jan 7;41(1):e14. doi: 10.1093/nar/gks830. Epub 2012 Sep 10.
FadE: whole genome methylation analysis for multiple sequencing platforms.
Souaiaia T1, Zhang Z, Chen T.
:: DESCRIPTION
Methpat summarises the resultant DNA methylation pattern data from the output of Bismark bismark_methylation_extractor.
::DEVELOPER
: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
epiPaleomix is a Fast, Accurate, and Automatic pipeline for generating nucleosome and methylation maps from high throughput sequencing data underlying ancient samples.
::DEVELOPER
The Centre for Anthropobiology and Genomics of Toulouse
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hanghoj K, Seguin-Orlando A, Schubert M, Madsen T, Pedersen JS, Willerslev E, Orlando L.
Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX.
Mol Biol Evol. 2016 Dec;33(12):3284-3298. doi: 10.1093/molbev/msw184. Epub 2016 Sep 13. PMID: 27624717; PMCID: PMC5100044.
