Introduction | Load DNAshapeR | Predict DNA shape features | Predict biophysical feature | Predict DNA shape feature due to CpG methylation | From FASTA file | From genomic intervals (e.g. TFs binding sites, CpG islands, replication origins, ...) | From public domain projects | From FASTA file with methylated DNA sequence | From FASTA and methylated position files | Visualize DNA shape prediction | Ensemble representation: metashape plot | Ensemble representation: heat map | Individual representation: genome browser-like tracks | Encode sequence and shape features | Encoding process | Showcase of statistical machine learning application | Session Info | References
Package: DNAshapeR 1.40.0
Tsu-Pei Chiu
DNAshapeR: High-throughput prediction of DNA shape features
DNAhapeR is an R/BioConductor package for ultra-fast, high-throughput predictions of DNA shape features. The package allows to predict, visualize and encode DNA shape features for statistical learning.
Authors:
DNAshapeR_1.40.0.tar.gz
DNAshapeR_1.40.0.zip(r-4.7-x86_64)DNAshapeR_1.40.0.zip(r-4.7-arm64)DNAshapeR_1.40.0.zip(r-4.6-x86_64)DNAshapeR_1.40.0.zip(r-4.6-arm64)DNAshapeR_1.40.0.zip(r-4.5-x86_64)
DNAshapeR_1.40.0.tgz(r-4.6-x86_64)DNAshapeR_1.40.0.tgz(r-4.6-arm64)DNAshapeR_1.40.0.tgz(r-4.5-x86_64)DNAshapeR_1.40.0.tgz(r-4.5-arm64)
DNAshapeR_1.40.0.tar.gz(r-4.7-arm64)DNAshapeR_1.40.0.tar.gz(r-4.7-x86_64)DNAshapeR_1.40.0.tar.gz(r-4.6-arm64)DNAshapeR_1.40.0.tar.gz(r-4.6-x86_64)
DNAshapeR_1.40.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DNAshapeR/json (API)
| # Install 'DNAshapeR' in R: |
| install.packages('DNAshapeR', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:DNAshapeR-1.41.0(bioc 3.24)DNAshapeR-1.40.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
structuralpredictiondna3dstructuresoftwarecpp
Last updated from:be1d392f7c (on RELEASE_3_23). Checks:1 ERROR, 13 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 222 | ||
| linux-devel-arm64 | NOTE | 301 | ||
| linux-devel-x86_64 | NOTE | 345 | ||
| source / vignettes | OK | 360 | ||
| linux-release-arm64 | NOTE | 290 | ||
| linux-release-x86_64 | NOTE | 415 | ||
| macos-release-arm64 | NOTE | 234 | ||
| macos-release-x86_64 | NOTE | 622 | ||
| macos-oldrel-arm64 | NOTE | 221 | ||
| macos-oldrel-x86_64 | NOTE | 449 | ||
| windows-devel-arm64 | NOTE | 847 | ||
| windows-devel-x86_64 | NOTE | 824 | ||
| windows-release-arm64 | NOTE | 710 | ||
| windows-release-x86_64 | NOTE | 472 | ||
| windows-oldrel-x86_64 | NOTE | 717 | ||
| wasm-release | OK | 211 |
Exports:encodeSeqShapegetFastagetShapeheatShapeplotShapereadShapetrackShape
Dependencies:BiocGenericsBiostringscrayondotCall64fieldsgenericsGenomicRangesIRangesmapsRColorBrewerRcppS4VectorsSeqinfospamviridisLiteXVector
