Package: methylMnM 1.51.0
Yan Zhou
methylMnM: detect different methylation level (DMR)
To give the exactly p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparation.
Authors:
methylMnM_1.51.0.tar.gz
methylMnM_1.51.0.zip(r-4.7)methylMnM_1.51.0.zip(r-4.6)methylMnM_1.51.0.zip(r-4.5)
methylMnM_1.51.0.tgz(r-4.6-x86_64)methylMnM_1.51.0.tgz(r-4.6-arm64)methylMnM_1.51.0.tgz(r-4.5-x86_64)methylMnM_1.51.0.tgz(r-4.5-arm64)
methylMnM_1.51.0.tar.gz(r-4.7-arm64)methylMnM_1.51.0.tar.gz(r-4.7-x86_64)methylMnM_1.51.0.tar.gz(r-4.6-arm64)methylMnM_1.51.0.tar.gz(r-4.6-x86_64)
methylMnM_1.51.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
methylMnM/json (API)
| # Install 'methylMnM' in R: |
| install.packages('methylMnM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:methylMnM-1.51.0(bioc 3.24)methylMnM-1.50.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwarednamethylationsequencing
Last updated from:192c6c89b5. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 189 | ||
| linux-devel-arm64 | NOTE | 177 | ||
| linux-devel-x86_64 | NOTE | 212 | ||
| source / vignettes | OK | 223 | ||
| linux-release-arm64 | NOTE | 151 | ||
| linux-release-x86_64 | NOTE | 201 | ||
| macos-release-arm64 | NOTE | 109 | ||
| macos-release-x86_64 | NOTE | 232 | ||
| macos-oldrel-arm64 | NOTE | 117 | ||
| macos-oldrel-x86_64 | NOTE | 152 | ||
| windows-devel | NOTE | 115 | ||
| windows-release | NOTE | 101 | ||
| windows-oldrel | NOTE | 96 | ||
| wasm-release | OK | 131 |
Exports:calcFactornewcalculatecountcalculatecount1calculatecountnegCNVnormalcountcpgbincountMeDIPbincountMREbincountMREcpgbincpgcountMnM.qvalueMnM.selectDMRMnM.testnormpdfnormpdft1pmultinomqvalue.rankremoveblacklist
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| MeDIP-Seq and MRE-Seq data analysis | methylMnM-package methylMnM |
| Normalization factor. | calcFactornew |
| Call C programs to R. | calculatecount |
| Call C programs to R. | calculatecount1 |
| Call C programs to R. | calculatecountneg |
| Normalize copy number variation (CNV). | CNVnormal |
| Compute the total CpG number of each bin with each CpG site. | countcpgbin |
| Compute the total MeDIP-seq number of each bin. | countMeDIPbin |
| Compute the total MRE-seq number of each bin. | countMREbin |
| Compute the MRE CpG number of each bin with MRE CpG sites. | countMREcpgbin |
| Call C programs to R. | cpgcount |
| Estimate the q-values for a given set of p-values | MnM.qvalue |
| Select significants of each comparation. | MnM.selectDMR |
| Compute p-value of each bin. | MnM.test |
| Compute p-value with normal distribution. | normpdf |
| Compute p-value with normal distribution. | normpdft1 |
| Call C programs to R. | pmultinom |
| Rank values. | qvalue.rank |
| Remove blacklist. | removeblacklist |