Introduction | Installation | Quick start | Input data | simPIC simulation | simPICcount class | Getting and setting parameters | Estimating Parameters | Simulating counts | Comparing Simulations and Real Data | Simulating Multiple Cell Types - equal proportions | Simulating Multiple Cell Types - variable proportions | Simulating Batch effects | Citing simPIC | Session information
Package: simPIC 1.8.0
Sagrika Chugh
simPIC: Flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data
simPIC is a package for simulating single-cell ATAC-seq count data. It provides a user-friendly, well documented interface for data simulation. Functions are provided for parameter estimation, realistic scATAC-seq data simulation, and comparing real and simulated datasets.
Authors:
simPIC_1.8.0.tar.gz
simPIC_1.8.0.zip(r-4.7-any)simPIC_1.8.0.zip(r-4.6-any)simPIC_1.8.0.zip(r-4.5-any)
simPIC_1.8.0.tgz(r-4.6-any)simPIC_1.8.0.tgz(r-4.5-any)
simPIC_1.8.0.tar.gz(r-4.7-any)simPIC_1.8.0.tar.gz(r-4.6-any)
simPIC_1.8.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
simPIC/json (API)
| # Install 'simPIC' in R: |
| install.packages('simPIC', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sagrikachugh/simpic/issues
On BioConductor:simPIC-1.9.0(bioc 3.24)simPIC-1.8.0(bioc 3.23)
singlecellatacseqsoftwaresequencingimmunooncologydataimportbioconductorbioinformaticsscatac-seqsimulation
Last updated from:401136b25b (on RELEASE_3_23). Checks:8 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 206 | ||
| linux-devel | NOTE | 386 | ||
| source / vignettes | OK | 300 | ||
| linux-release | NOTE | 369 | ||
| macos-release | NOTE | 376 | ||
| macos-oldrel | NOTE | 253 | ||
| windows-devel | NOTE | 285 | ||
| windows-release | NOTE | 274 | ||
| windows-oldrel | NOTE | 269 | ||
| wasm-release | OK | 144 |
Exports:newsimPICcountsetsimPICparameterssimPICcomparesimPICestimatesimPICgetsimPICgetparameterssimPICsimulatesimPICsimulatemultisimPICsimulatesingle
Dependencies:abindactuarassortheadbackportsbeachmatBHBiobaseBiocGenericsBiocParallelcheckmateclicodetoolscpp11DelayedArrayedgeRexpintfarverfitdistrplusformatRfutile.loggerfutile.optionsgenericsGenomicRangesglueIRangeslabelinglambda.rlatticelifecyclelimmalocfitMASSMatrixMatrixGenericsmatrixStatsR6RColorBrewerRcpprlangS4ArraysS4VectorsscalesscuttleSeqinfoSingleCellExperimentsnowSparseArraystatmodSummarizedExperimentsurvivalviridisLitewithrXVector
