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sccomp

This is the development version of sccomp; for the stable release version, see sccomp.

Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data


Bioconductor version: Development (3.19)

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 (from within R, enter citation("sccomp")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
New sccomp framework HTML R Script
Overview of the sccomp package HTML R Script
Reference Manual PDF

Details

biocViews Clustering, GeneExpression, ImmunoOncology, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.7.5
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-3
Depends R (>= 4.2.0)
Imports methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstantools (>= 2.1.1), rstan (>= 2.26.0), SeuratObject, SingleCellExperiment, parallel, dplyr, tidyr, purrr, magrittr, rlang, tibble, boot, lifecycle, stats, tidyselect, utils, ggplot2, ggrepel, patchwork, forcats, readr, scales, stringr, glue
System Requirements GNU make
URL https://github.com/stemangiola/sccomp
Bug Reports https://github.com/stemangiola/sccomp/issues
See More
Suggests BiocStyle, testthat (>= 3.0.0), markdown, knitr, loo, tidyseurat, tidySingleCellExperiment
Linking To BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.26.0), StanHeaders (>= 2.26.0)
Enhances furrr, extraDistr
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 sccomp_1.7.5.tar.gz
Windows Binary sccomp_1.7.5.zip
macOS Binary (x86_64) sccomp_1.7.5.tgz
macOS Binary (arm64) sccomp_1.7.2.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