├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS ├── R ├── SRTaffine.R ├── SRTcci.R ├── SRTcount.R ├── SRTfit.R ├── SRTmodels.R ├── SRTsim_class.R ├── body.R ├── compareSRT.R ├── createSRT.R ├── data.R ├── globals.R ├── reGenCountshiny.R ├── runapp.R ├── server.R ├── shiny2srt.R ├── sidebar.R ├── simSRTLocs.R ├── subsetSRT.R ├── ui.R ├── utilies_func.R ├── visualize_gene.R └── visualize_metrics.R ├── README.md ├── data ├── exampleLIBD.rda ├── toyData.rda └── toyShiny.rda ├── docs ├── 01_about.md ├── Figure1_long_noblock_update.png ├── README.md ├── _config.yml ├── index.md ├── pages │ ├── 02_Reference_Based_Example.md │ ├── 03_Reference_Free_Example.md │ ├── 04_Reproduce.md │ ├── 05_installation.md │ ├── metrics_violin.png │ ├── pattern_gene1.png │ ├── pattern_gene2.png │ ├── shiny1.png │ ├── shiny2.png │ ├── shiny3.png │ ├── shiny4.png │ └── shiny5.png └── style.css ├── index.md ├── man ├── EstParam.Rd ├── SRTsim_shiny.Rd ├── Shiny2SRT.Rd ├── compareSRT.Rd ├── convert_grid.Rd ├── createSRT.Rd ├── exampleLIBD.Rd ├── fit_pos_optim.Rd ├── get_metrics_pd.Rd ├── get_stats_gene.Rd ├── get_stats_loc.Rd ├── metaParam.Rd ├── reGenCountshiny.Rd ├── refCounts.Rd ├── refcolData.Rd ├── refrowData.Rd ├── simCounts.Rd ├── simNewLocs.Rd ├── simcolData.Rd ├── simrowData.Rd ├── srtsim_cci_free.Rd ├── srtsim_cci_ref.Rd ├── srtsim_count.Rd ├── srtsim_count_affine.Rd ├── srtsim_fit.Rd ├── srtsim_newlocs.Rd ├── subsetSRT.Rd ├── toyData.Rd ├── toyShiny.Rd ├── visualize_gene.Rd └── visualize_metrics.Rd └── vignettes ├── .Rhistory └── SRTsim.Rmd /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzhoulab/SRTsim/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xzhoulab/SRTsim/HEAD/LICENSE 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