Software | Definitions | Copy Number | Cellular prevalence | Variant Allele Frequency | Simulation | Optimization | Known configuration | Unknown configuration | Downstream Applications | Session Info | References
Package: SMASH 1.0.0
Paul Little
SMASH: Subclone Multiplicity Allocation and Somatic Heterogeneity
Cluster user-supplied somatic read counts with corresponding allele-specific copy number and tumor purity to infer feasible underlying intra-tumor heterogeneity in terms of number of subclones, multiplicity, and allocation (Little et al. (2019) <doi:10.1186/s13073-019-0643-9>).
Authors:
SMASH_1.0.0.tar.gz
SMASH_1.0.0.tar.gz(r-4.7-arm64)SMASH_1.0.0.tar.gz(r-4.7-x86_64)SMASH_1.0.0.tar.gz(r-4.6-arm64)SMASH_1.0.0.tar.gz(r-4.6-x86_64)
SMASH_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
SMASH/json (API)
| # Install 'SMASH' in R: |
| install.packages('SMASH', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Uses libs:
Datasets:
- eS - A collection of pre-defined subclone configurations.
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:f73c872758. Checks:6 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 159 | ||
| linux-devel-x86_64 | OK | 180 | ||
| source / vignettes | OK | 278 | ||
| linux-release-arm64 | OK | 176 | ||
| linux-release-x86_64 | OK | 182 | ||
| wasm-release | OK | 170 |
Exports:gen_ITH_RDgen_subj_truthgrid_ITH_optimITH_optimvis_GRID
Dependencies:askpassbase64encbitopsbrewbriobslibcachemcallrcaToolsclicliprcommonmarkcpp11crayoncredentialscurldescdevtoolsdiffobjdigestdownlitellipsisevaluatefansifarverfastmapfontawesomefsgertggplot2gitcredsgluegplotsgtablegtoolshighrhtmltoolshtmlwidgetshttpuvhttr2iniisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlifecyclemagrittrmemoisemimeminiUIopensslotelpakpillarpkgbuildpkgconfigpkgdownpkgloadplyrpraiseprettyunitsprocessxprofvispromisespspurrrR6raggrappdirsrcmdcheckRColorBrewerRcppRcppArmadilloRCurlreshape2rlangrmarkdownroxygen2rprojrootrstudioapirversionsS7sassscalessessioninfoshinysmartersourcetoolsstringistringrsyssystemfontstestthattextshapingtibbletinytexurlcheckerusethisutf8vctrsviridisLitewaldowhiskerwithrxfunxml2xopenxtableyamlzip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| A collection of pre-defined subclone configurations. | eS |
| gen_ITH_RD | gen_ITH_RD |
| gen_subj_truth | gen_subj_truth |
| grid_ITH_optim | grid_ITH_optim |
| ITH_optim | ITH_optim |
| vis_GRID | vis_GRID |