Package: simPIC 1.3.0

Sagrika Chugh

simPIC: 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:Sagrika Chugh [aut, cre], Davis McCarthy [aut], Heejung Shim [aut]

simPIC_1.3.0.tar.gz
simPIC_1.3.0.zip(r-4.5)simPIC_1.3.0.zip(r-4.4)simPIC_1.1.0.zip(r-4.3)
simPIC_1.3.0.tgz(r-4.4-any)simPIC_1.1.0.tgz(r-4.3-any)
simPIC_1.3.0.tar.gz(r-4.5-noble)simPIC_1.3.0.tar.gz(r-4.4-noble)
simPIC_1.3.0.tgz(r-4.4-emscripten)simPIC_1.1.0.tgz(r-4.3-emscripten)
simPIC.pdf |simPIC.html✨
simPIC/json (API)
NEWS

# Install 'simPIC' in R:

install.packages('simPIC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sagrikachugh/simpic/issues

On BioConductor:simPIC-1.3.0(bioc 3.21)simPIC-1.2.0(bioc 3.20)

singlecell atacseq software sequencing immunooncology dataimport

4.54 score 3 scripts 120 downloads 7 exports 61 dependencies

Last updated 2 months agofrom:17e7089482. Checks:OK: 5 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 03 2024
R-4.5-win	NOTE	Dec 03 2024
R-4.5-linux	NOTE	Dec 03 2024
R-4.4-win	OK	Dec 03 2024
R-4.4-mac	OK	Dec 03 2024
R-4.3-win	OK	Sep 22 2024
R-4.3-mac	OK	Sep 22 2024

Exports:newsimPICcount setsimPICparameters simPICcompare simPICestimate simPICget simPICgetparameters simPICsimulate

Dependencies:abind actuar askpass assorthead backports beachmat BH Biobase BiocGenerics BiocParallel checkmate cli codetools colorspace cpp11 crayon curl DelayedArray expint farver fitdistrplus formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges glue httr IRanges jsonlite labeling lambda.r lattice lifecycle MASS Matrix MatrixGenerics matrixStats mime munsell openssl R6 RColorBrewer Rcpp rlang S4Arrays S4Vectors scales scuttle SingleCellExperiment snow SparseArray SummarizedExperiment survival sys UCSC.utils viridisLite XVector zlibbioc

simPIC: simulating single-cell ATAC-seq data

Sagrika Chugh

Rendered fromvignette.Rmdusingknitr::rmarkdownon Dec 03 2024.

Last update: 2024-03-18
Started: 2024-02-28

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add feature statistics	addFeatureStats
Convert Sparse Matrix to SingleCellExperiment object	convert_to_SCE
Get counts from Single Cell Experiment object	getCounts
simPIC: Simulate single-cell ATAC-seq data	global
newsimPICcount	newsimPICcount
Custom theme for ggplot2	plot_theme
Bind rows (matched)	rbindMatched
Select fit	selectFit
Set simPIC parameters	setsimPICparameters
Compare SingleCellExperiment objects	simPICcompare
The simPICcount class	simPICcount simPICcount-class
Estimate simPIC simulation parameters	simPICestimate simPICestimate.dgCMatrix simPICestimate.SingleCellExperiment
Estimate simPIC library size parameters.	simPICestimateLibSize
Estimate simPIC peak means	simPICestimatePeakMean
Estimate simPIC peak sparsity.	simPICestimateSparsity
Get a single simPICcount parameter	simPICget
Get parameters	simPICgetparameters
simPIC simulation	simPICsimulate
Simulate simPIC library sizes	simPICsimulateLibSize
Simulate simPIC peak means.	simPICsimulatePeakMean
Simulate true counts.	simPICsimulateTrueCounts