sccomp
Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data
Bioconductor version: Release (3.17)
A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model can infer changes in tissue composition and heterogeneity, and can produce realistic data simulations based on any existing dataset. This model can also transfer knowledge from a large set of integrated datasets to increase accuracy further.
Author: Stefano Mangiola [aut, cre]
Maintainer: Stefano Mangiola <mangiolastefano at gmail.com>
citation("sccomp")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("sccomp")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("sccomp")| Overview of the sccomp package | HTML | R Script |
| Reference Manual |
Details
| biocViews | Clustering, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (1.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.2.0) |
| Imports | methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstantools (>= 2.1.1), rstan (>= 2.18.1), SeuratObject, SingleCellExperiment, parallel, dplyr, tidyr, purrr, magrittr, rlang, tibble, boot, lifecycle, stats, tidyselect, utils, ggplot2, ggrepel, patchwork, forcats, readr, scales, stringr, glue |
| Linking To | BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) |
| Suggests | BiocStyle, testthat (>= 3.0.0), markdown, knitr, tidyseurat, tidySingleCellExperiment, loo |
| System Requirements | GNU make |
| Enhances | furrr, extraDistr |
| URL | https://github.com/stemangiola/sccomp |
| Bug Reports | https://github.com/stemangiola/sccomp/issues |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | sccomp_1.4.0.tar.gz |
| Windows Binary | sccomp_1.4.0.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | sccomp_1.3.5.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/sccomp |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/sccomp |
| Bioc Package Browser | https://code.bioconductor.org/browse/sccomp/ |
| Package Short Url | https://bioconductor.org/packages/sccomp/ |
| Package Downloads Report | Download Stats |