Package: SCRIP 1.0.0
Fei Qin
SCRIP: An Accurate Simulator for Single-Cell RNA Sequencing Data
We provide a comprehensive scheme that is capable of simulating Single Cell RNA Sequencing data for various parameters of Biological Coefficient of Variation, busting kinetics, differential expression (DE), cell or sample groups, cell trajectory, batch effect and other experimental designs. 'SCRIP' proposed and compared two frameworks with Gamma-Poisson and Beta-Gamma-Poisson models for simulating Single Cell RNA Sequencing data. Other reference is available in Zappia et al. (2017) <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1305-0>.
Authors:
SCRIP_1.0.0.tar.gz
SCRIP_1.0.0.zip(r-4.5)SCRIP_1.0.0.zip(r-4.4)SCRIP_1.0.0.zip(r-4.3)
SCRIP_1.0.0.tgz(r-4.4-any)SCRIP_1.0.0.tgz(r-4.3-any)
SCRIP_1.0.0.tar.gz(r-4.5-noble)SCRIP_1.0.0.tar.gz(r-4.4-noble)
SCRIP_1.0.0.tgz(r-4.4-emscripten)
SCRIP.pdf |SCRIP.html✨
SCRIP/json (API)
| # Install 'SCRIP' in R: |
| install.packages('SCRIP', repos = c('https://thecailab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/thecailab/scrip/issues
- acinar.data - Parameter files estimated from acinar.data using splatEstimate
- params_acinar - A data frame with 1000 genes and 80 cells
Last updated 2 years agofrom:3d9c103414. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 27 2024 |
| R-4.5-win | WARNING | Sep 27 2024 |
| R-4.5-linux | WARNING | Oct 27 2024 |
| R-4.4-win | WARNING | Oct 27 2024 |
| R-4.4-mac | WARNING | Oct 27 2024 |
| R-4.3-win | WARNING | Oct 27 2024 |
| R-4.3-mac | WARNING | Oct 27 2024 |
Exports:SCRIPsimusimu_clustersimu_DEsimu.VEGs
Dependencies:abindaskpassassortheadbackportsbase64encbeachmatBHBiobaseBiocGenericsBiocManagerBiocParallelbitopsbslibcachemcaToolscheckmatecliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDelayedArraydeldirdigestdotCall64dplyrdqrngedgeRevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomeformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenlifecyclelimmalistenvlmtestlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsneS4ArraysS4VectorssassscalesscattermoresctransformscuttleSeuratSeuratObjectshinySingleCellExperimentsitmosnowsourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilssplatterstatmodstringistringrSummarizedExperimentsurvivalsystensortibbletidyrtidyselecttinytexUCSC.utilsutf8uwotvctrsviridisLitewithrxfunxtableXVectoryamlzlibbioczoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| parameter files estimated from acinar.data using splatEstimate | acinar.data |
| Brownian bridge | bridge |
| Bring items forward | bringItemsForward |
| Get log-normal factors | getLNormFactors |
| Get path order | getPathOrder |
| Logistic function | logistic |
| A data frame with 1000 genes and 80 cells | params_acinar |
| Simulate batch means | SCRIPsimBatchCellMeans |
| Simulate batch effects | SCRIPsimBatchEffects |
| Simulate BCV means | SCRIPsimBCVMeans |
| Simulate dropout | SCRIPsimDropout |
| Simulate gene means | SCRIPsimGeneMeans |
| Simulate Group CellMeans | SCRIPsimGroupCellMeans |
| Simulate group differential expression | SCRIPsimGroupDE |
| Simulate library sizes | SCRIPsimLibSizes |
| sim PathCellMeans | SCRIPsimPathCellMeans |
| Sim PathDE | SCRIPsimPathDE |
| Simulate cell means | SCRIPsimSingleCellMeans |
| Simulate true counts | SCRIPsimTrueCounts |
| SCRIP simulation | SCRIPsimu |
| SCRIP simulation for clustering analysis with multiple cell types | simu_cluster |
| SCRIP simulation for differential expression | simu_DE |
| SCRIP simulation for clustering analysis | simu.VEGs |
