Package: gkmSVM 0.83.0
gkmSVM: Gapped-Kmer Support Vector Machine
Imports the 'gkmSVM' v2.0 functionalities into R <https://www.beerlab.org/gkmsvm/> It also uses the 'kernlab' library (separate R package by different authors) for various SVM algorithms. Users should note that the suggested packages 'rtracklayer', 'GenomicRanges', 'BSgenome', 'BiocGenerics', 'Biostrings', 'GenomeInfoDb', 'IRanges', and 'S4Vectors' are all BioConductor packages <https://bioconductor.org>.
Authors:
gkmSVM_0.83.0.tar.gz
gkmSVM_0.83.0.zip(r-4.5)gkmSVM_0.83.0.zip(r-4.4)gkmSVM_0.83.0.zip(r-4.3)
gkmSVM_0.83.0.tgz(r-4.4-x86_64)gkmSVM_0.83.0.tgz(r-4.4-arm64)gkmSVM_0.83.0.tgz(r-4.3-x86_64)gkmSVM_0.83.0.tgz(r-4.3-arm64)
gkmSVM_0.83.0.tar.gz(r-4.5-noble)gkmSVM_0.83.0.tar.gz(r-4.4-noble)
gkmSVM_0.83.0.tgz(r-4.4-emscripten)gkmSVM_0.83.0.tgz(r-4.3-emscripten)
gkmSVM.pdf |gkmSVM.html✨
gkmSVM/json (API)
| # Install 'gkmSVM' in R: |
| install.packages('gkmSVM', repos = c('https://mbeer3.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 1 years agofrom:e7b29da8ef. Checks:OK: 6 NOTE: 3. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 27 2024 |
| R-4.5-win-x86_64 | OK | Oct 27 2024 |
| R-4.5-linux-x86_64 | OK | Oct 27 2024 |
| R-4.4-win-x86_64 | OK | Oct 27 2024 |
| R-4.4-mac-x86_64 | NOTE | Oct 27 2024 |
| R-4.4-mac-aarch64 | NOTE | Oct 27 2024 |
| R-4.3-win-x86_64 | OK | Oct 27 2024 |
| R-4.3-mac-x86_64 | OK | Oct 27 2024 |
| R-4.3-mac-aarch64 | NOTE | Oct 27 2024 |
Exports:genNullSeqsgkmsvm_classifygkmsvm_deltagkmsvm_kernelgkmsvm_traingkmsvm_trainCV
Dependencies:ade4bitopscaToolsgplotsgtoolskernlabKernSmoothlatticeMASSnlmepixmapRcppRcppArmadilloROCRsegmentedseqinrsp
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Gapped-Kmer Support Vector Machine | gkmSVM-package gkmSVM |
| Generating GC/repeat matched randomly selected genomic sequences for the negative set | genNullSeqs |
| Classifying(/scoring) new sequences using the gkmSVM model | gkmsvm_classify |
| Calculating deltaSVM scores | gkmsvm_delta |
| Computing the kernel matrix | gkmsvm_kernel |
| Training the SVM model | gkmsvm_train |
| Training the SVM model, using repeated CV to tune parameter C and plot ROC curves | gkmsvm_trainCV |
