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:Paul Little [aut, cre]

SMASH_1.0.0.tar.gz
SMASH_1.0.0.tar.gz(r-4.5-noble)SMASH_1.0.0.tar.gz(r-4.4-noble)
SMASH_1.0.0.tgz(r-4.4-emscripten)SMASH_1.0.0.tgz(r-4.3-emscripten)
SMASH.pdf |SMASH.html✨
SMASH/json (API)

# Install 'SMASH' in R:
install.packages('SMASH', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • eS - A collection of pre-defined subclone configurations.

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

openblascppopenmp

2.00 score 5 exports 119 dependencies

Last updated 25 days agofrom:f73c872758. Checks:2 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 27 2025
R-4.5-linux-x86_64OKFeb 27 2025

Exports:gen_ITH_RDgen_subj_truthgrid_ITH_optimITH_optimvis_GRID

Dependencies:askpassbase64encbitopsbrewbriobslibcachemcallrcaToolsclicliprcolorspacecommonmarkcpp11crayoncredentialscurldescdevtoolsdiffobjdigestdownlitellipsisevaluatefansifarverfastmapfontawesomefsgertggplot2ghgitcredsgluegplotsgtablegtoolshighrhtmltoolshtmlwidgetshttpuvhttr2iniisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimeminiUImunsellnlmeopensslpillarpkgbuildpkgconfigpkgdownpkgloadplyrpraiseprettyunitsprocessxprofvispromisespspurrrR6raggrappdirsrcmdcheckRColorBrewerRcppRcppArmadilloRCurlremotesreshape2rlangrmarkdownroxygen2rprojrootrstudioapirversionssassscalessessioninfoshinysmartersourcetoolsstringistringrsyssystemfontstestthattextshapingtibbletinytexurlcheckerusethisutf8vctrsviridisLitewaldowhiskerwithrxfunxml2xopenxtableyamlzip

Introduction

Paul Little

Rendered fromintro.Rmdusingknitr::rmarkdownon Feb 27 2025.

Last update: 2025-02-27
Started: 2025-02-27