simPIC
This is the released version of simPIC; for the devel version, see simPIC.
Flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data
Bioconductor version: Release (3.23)
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.
Author: Sagrika Chugh [aut, cre]
, Heejung Shim [aut], Davis McCarthy [aut]
Maintainer: Sagrika Chugh <sagrika.chugh at gmail.com>
citation("simPIC")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("simPIC")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("simPIC")| simPIC: simulating single-cell ATAC-seq data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, DataImport, ImmunoOncology, Sequencing, SingleCell, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.5.0), SingleCellExperiment |
| Imports | BiocGenerics, checkmate (>= 2.0.0), fitdistrplus, matrixStats, actuar, Matrix, stats, SummarizedExperiment, rlang, S4Vectors, methods, scales, scuttle, edgeR, withr |
| System Requirements | |
| URL | https://github.com/sagrikachugh/simPIC |
| Bug Reports | https://github.com/sagrikachugh/simPIC/issues |
See More
| Suggests | ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), scater, scran, magick |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | simPIC_1.8.0.tar.gz |
| Windows Binary (x86_64) | simPIC_1.8.0.zip |
| macOS Binary (big-sur-x86_64) | simPIC_1.8.0.tgz |
| macOS Binary (sonoma-arm64) | simPIC_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/simPIC |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/simPIC |
| Bioc Package Browser | https://code.bioconductor.org/browse/simPIC/ |
| Package Short Url | https://bioconductor.org/packages/simPIC/ |
| Package Downloads Report | Download Stats |