Introduction | Current Features | Major improvements | v1.16 [BioC 3.21] | Reading data | Using data from NCBI GEO | Using Bismark cytosine report files | Simulating data | AMR identification | AMR annotation and enrichment analysis | Other information | Citing the ramr package | The data underlying ramr manuscript | Session Info
Package: ramr 1.21.3
Oleksii Nikolaienko
ramr: Detection of Rare Aberrantly Methylated Regions in Array and NGS Data
ramr is an R package for detection of epimutations (i.e., infrequent aberrant DNA methylation events) in large data sets obtained by methylation profiling using array or high-throughput methylation sequencing. In addition, package provides functions to visualize found aberrantly methylated regions (AMRs), to generate sets of all possible regions to be used as reference sets for enrichment analysis, and to generate biologically relevant test data sets for performance evaluation of AMR/DMR search algorithms.
Authors:
ramr_1.21.3.tar.gz
ramr_1.21.3.zip(r-4.7-x86_64)ramr_1.21.3.zip(r-4.7-arm64)ramr_1.21.3.zip(r-4.6-x86_64)ramr_1.21.3.zip(r-4.6-arm64)ramr_1.21.3.zip(r-4.5-x86_64)
ramr_1.21.3.tgz(r-4.6-x86_64)ramr_1.21.3.tgz(r-4.6-arm64)ramr_1.21.3.tgz(r-4.5-x86_64)ramr_1.21.3.tgz(r-4.5-arm64)
ramr_1.21.3.tar.gz(r-4.7-arm64)ramr_1.21.3.tar.gz(r-4.7-x86_64)ramr_1.21.3.tar.gz(r-4.6-arm64)ramr_1.21.3.tar.gz(r-4.6-x86_64)
ramr_1.21.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ramr/json (API)
| # Install 'ramr' in R: |
| install.packages('ramr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bbcg/ramr/issues
Datasets:
- ramr.data - Simulated Illumina HumanMethylation 450k data set with 3000 CpGs and 100 samples
- ramr.samples - Simulated Illumina HumanMethylation 450k data set with 3000 CpGs and 100 samples
- ramr.tp.nonunique - Simulated Illumina HumanMethylation 450k data set with 3000 CpGs and 100 samples
- ramr.tp.unique - Simulated Illumina HumanMethylation 450k data set with 3000 CpGs and 100 samples
On BioConductor:ramr-1.21.3(bioc 3.24)ramr-1.20.2(bioc 3.23)
dnamethylationdifferentialmethylationepigeneticsmethylationarraymethylseqaberrant-methylationbioconductordna-methylationepimutationmethylation-microarraysnext-generation-sequencingcppopenmp
Last updated from:38eacd491b. Checks:14 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 232 | ||
| linux-devel-arm64 | NOTE | 361 | ||
| linux-devel-x86_64 | NOTE | 419 | ||
| source / vignettes | OK | 434 | ||
| linux-release-arm64 | NOTE | 355 | ||
| linux-release-x86_64 | NOTE | 426 | ||
| macos-release-arm64 | NOTE | 261 | ||
| macos-release-x86_64 | NOTE | 494 | ||
| macos-oldrel-arm64 | NOTE | 322 | ||
| macos-oldrel-x86_64 | NOTE | 824 | ||
| windows-devel-arm64 | NOTE | 647 | ||
| windows-devel-x86_64 | NOTE | 391 | ||
| windows-release-arm64 | NOTE | 440 | ||
| windows-release-x86_64 | NOTE | 358 | ||
| windows-oldrel-x86_64 | NOTE | 367 | ||
| wasm-release | OK | 197 |
Exports:getAMRgetAMR.obsoletegetUniverseplotAMRsimulateAMRsimulateDatasimulateData.obsolete
Dependencies:BiocGenericsdata.tablegenericsGenomicRangesIRangesRcppS4VectorsSeqinfo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Search for aberrantly methylated regions | getAMR |
| [OBSOLETE] Search for aberrantly methylated regions | getAMR.obsolete |
| Merges, filters and outputs all genomic regions of a given `GRanges` object | getUniverse |
| Plot aberrantly methylated regions | plotAMR |
| Simulated Illumina HumanMethylation 450k data set with 3000 CpGs and 100 samples | ramr.data ramr.samples ramr.tp.nonunique ramr.tp.unique |
| Simulate a set of aberrantly methylated regions | simulateAMR |
| Template-based simulation of methylation data sets | simulateData |
| [OBSOLETE] Template-based simulation of methylation data sets | simulateData.obsolete |