• IMA

  • Referenced in 5 articles [sw23822]
  • high-density microarray for quantifying the methylation level of over 450 000 CpG sites within ... human genome. Illumina Methylation Analyzer (IMA) is a computational package designed to automate the pipeline ... summarization of site-level and region-level methylation changes in epigenetic studies utilizing the 450K...
  • MethylSig

  • Referenced in 4 articles [sw23506]
  • incorporate local information to improve group methylation level and/or variance estimation for experiments with small...
  • methyAnalysis

  • Referenced in 2 articles [sw30268]
  • also includes functions of estimating the methylation levels from Methy-Seq data...
  • iLM-2L

  • Referenced in 2 articles [sw16853]
  • level predictor for identifying protein lysine methylation sites and their methylation degrees by incorporating ... without considering its methylation degrees. In this paper, a novel two-level predictor named ... predict lysine methylation sites and their methylation degrees using composition of k-spaced amino acid ... lysine residue is a methylation site, and the 2nd level is to identify which methylation...
  • MethPipe

  • Referenced in 1 article [sw30174]
  • mapping bisulfite sequencing reads and estimating methylation levels at individual cytosine sites. MethPipe also includes ... tools for identifying higher-level methylation features, including hypo-methylated regions (HMR), partially methylated domains...
  • MethylPurify

  • Referenced in 1 article [sw31457]
  • regions with bisulfite reads showing discordant methylation levels to infer tumor purity from tumor samples...
  • iRNA-PseKNC

  • Referenced in 1 article [sw27658]
  • nucleotide accept a methyl group. This methylation process is a post-transcriptional modification, which occurs ... post-transcriptional level. Through biochemical experiments 2’-O-methylation sites produce good results but these...
  • CodonO

  • Referenced in 2 articles [sw17252]
  • level, genetic coding error minimization, mRNA stability, codon context, tRNA richness, CpG suppression, DNA methylation...
  • BSMAP

  • Referenced in 5 articles [sw23515]
  • thymine alignments, and multiple CpG heterogeneous methylation. RESULTS: We developed an efficient bisulfite reads mapping ... high-throughput bisulfite reads at whole genome level with feasible memory and CPU usage...
  • Bisulfighter

  • Referenced in 3 articles [sw23508]
  • sample, and to detect differentially methylated regions (DMRs) between paired samples. Although numerous tools have ... false positives, more precise estimates of mC levels, more exact locations of DMRs and better...
  • metilene

  • Referenced in 1 article [sw28768]
  • allows the detection of DMRs in large methylation experiments with multiple groups of samples ... systems biology on a global, genome-wide level. Whether in the framework of international consortia...
  • MLML

  • Referenced in 1 article [sw30173]
  • MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylation. Motivation: The two major epigenetic modifications ... estimates of 5-mC or 5-hmC levels. Results: We present a method to jointly...
  • MethCP

  • Referenced in 1 article [sw28729]
  • challenge in identifying regions that are differentially methylated (DMRs) between different conditions. Many methods have ... naturally segments the genome and provides region-level differential analysis. For simple two-group comparison ... time-course data on another dataset following methylation throughout seed germination in Arabidopsis. Availability...
  • Mathematica

  • Referenced in 6337 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • Matlab

  • Referenced in 13460 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • R

  • Referenced in 9810 articles [sw00771]
  • R is a language and environment for statistical...
  • RODAS

  • Referenced in 1695 articles [sw04112]
  • Rosenbrock method of order 4(3), for problems...
  • Bioconductor

  • Referenced in 320 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension...
  • WinBUGS

  • Referenced in 764 articles [sw04492]
  • WinBUGS is part of the BUGS project, which...
  • ggplot2

  • Referenced in 352 articles [sw04557]
  • R package ggplot2: An implementation of the Grammar...