Introduction | Worked examples | Publicly available array data: oxBS and BS methods | Publicly available array data: TAB and BS methods | Publicly available sequencing data: oxBS and BS methods | Simulated data | BS and oxBS methods | BS and TAB methods | oxBS and TAB methods | BS, oxBS and TAB methods | References
Package: MLML2R 0.3.3
MLML2R: Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions
Maximum likelihood estimates (MLE) of the proportions of 5-mC and 5-hmC in the DNA using information from BS-conversion, TAB-conversion, and oxBS-conversion methods. One can use information from all three methods or any combination of two of them. Estimates are based on Binomial model by Qu et al. (2013) <doi:10.1093/bioinformatics/btt459> and Kiihl et al. (2019) <doi:10.1515/sagmb-2018-0031>.
Authors:
MLML2R_0.3.3.tar.gz
MLML2R_0.3.3.zip(r-4.7)MLML2R_0.3.3.zip(r-4.6)MLML2R_0.3.3.zip(r-4.5)
MLML2R_0.3.3.tgz(r-4.6-any)MLML2R_0.3.3.tgz(r-4.5-any)
MLML2R_0.3.3.tar.gz(r-4.7-any)MLML2R_0.3.3.tar.gz(r-4.6-any)
MLML2R_0.3.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MLML2R/json (API)
| # Install 'MLML2R' in R: |
| install.packages('MLML2R', repos = c('https://samarafk.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/samarafk/mlml2r/issues
Datasets:
- C_BS_sim - C (unconverted) counts from BS
- C_OxBS_sim - C (unconverted) counts from oxBS
- C_TAB_sim - C (unconverted) counts from TAB
- T_BS_sim - T (converted) counts from BS
- T_OxBS_sim - T (converted) counts from oxBS
- T_TAB_sim - T (converted) counts from TAB
softwaremethylationarrayepigeneticsdnamethylationmicroarraytwochannelonechannel
Last updated from:f113831f46. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 184 | ||
| source / vignettes | OK | 280 | ||
| linux-release-x86_64 | OK | 228 | ||
| macos-release-arm64 | OK | 148 | ||
| macos-oldrel-arm64 | OK | 168 | ||
| windows-devel | OK | 131 | ||
| windows-release | OK | 113 | ||
| windows-oldrel | OK | 136 | ||
| wasm-release | OK | 167 |
Exports:MLML
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| C (unconverted) counts from BS | C_BS_sim |
| C (unconverted) counts from oxBS | C_OxBS_sim |
| C (unconverted) counts from TAB | C_TAB_sim |
| MLE (maximum likelihood estimates) of 5-mC and 5-hmC levels. | MLML |
| T (converted) counts from BS | T_BS_sim |
| T (converted) counts from oxBS | T_OxBS_sim |
| T (converted) counts from TAB | T_TAB_sim |
