Introduction | The ActiveDriverWGS Model | Publication | Input Data | Mutations | Elements and Sites | Example | Importing BED12 & BED4 Files as Input Regions | Basic Use | Parameter Interpretation | Interpreting the Results | Multiple Testing Corrections | Adapting ActiveDriverWGS to High Performance Computing Clusters | 1. format_muts | 2. ADWGS_test | Technical Support
Package: ActiveDriverWGS 1.2.1
ActiveDriverWGS: A Driver Discovery Tool for Cancer Whole Genomes
A method for finding enrichments of somatic single nucleotide variants (SNVs) and small insertions-deletions (Indels) in functional elements in the human genome. 'ActiveDriverWGS' detects coding and noncoding cancer driver elements using whole genome sequencing data. The method is part of the publication H. Zhu et al. (2020) <doi:10.1016/j.molcel.2019.12.027> "Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks" in Molecular Cell.
Authors:
ActiveDriverWGS_1.2.1.tar.gz
ActiveDriverWGS_1.2.1.zip(r-4.7-any)ActiveDriverWGS_1.2.1.zip(r-4.6-any)ActiveDriverWGS_1.2.1.zip(r-4.5-any)
ActiveDriverWGS_1.2.1.tgz(r-4.6-any)ActiveDriverWGS_1.2.1.tgz(r-4.5-any)
ActiveDriverWGS_1.2.1.tar.gz(r-4.7-any)ActiveDriverWGS_1.2.1.tar.gz(r-4.6-any)
ActiveDriverWGS_1.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ActiveDriverWGS/json (API)
| # Install 'ActiveDriverWGS' in R: |
| install.packages('ActiveDriverWGS', repos = c('https://reimand0.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- cancer_gene_sites - Post-translational modification sites found in cancer genes
- cancer_genes - Cancer_genes
- cll_mutations - CLL mutations
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:c53bb4f686. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 376 | ||
| source / vignettes | OK | 400 | ||
| linux-release-x86_64 | OK | 334 | ||
| macos-release-arm64 | OK | 465 | ||
| macos-oldrel-arm64 | OK | 316 | ||
| windows-devel | OK | 266 | ||
| windows-release | OK | 280 | ||
| windows-oldrel | OK | 251 | ||
| wasm-release | OK | 334 |
Exports:ActiveDriverWGSADWGS_testformat_mutsprepare_elements_from_BED12prepare_elements_from_BED4
Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomecigarillocodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RCurlrestfulrRhtslibrjsonRsamtoolsrtracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysUCSC.utilsXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| fix_all_results verifies that the results table has the correct format and p-values | .fix_all_results |
| This function finds the tri-nucleotide context of mutations | .get_3n_context_of_mutations |
| Calculates the number of expected mutations based | .get_obs_exp |
| Returns significant results | .get_signf_results |
| Makes mutational signatures | .make_mut_signatures |
| Splits a BED12 file into separate regions | .split_coord_fragments_in_BED |
| ActiveDriverWGS is a driver discovery tool for simple somatic mutations in cancer whole genomes | ActiveDriverWGS |
| ADWGS_test executes the statistical test for ActiveDriverWGS | ADWGS_test |
| post-translational modification sites found in cancer genes | cancer_gene_sites |
| cancer_genes | cancer_genes |
| CLL mutations | cll_mutations |
| This function filters hypermutated samples and returns the formatted mutations with the appropriate trinucleotide context | format_muts |
| Prepares element coords from a BED12 file | prepare_elements_from_BED12 |
| Prepares element coords from a BED4 file | prepare_elements_from_BED4 |
