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Bioconductor - sccomp (development version)

sccomp

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

Tests differences in cell-type proportion for single-cell data, robust to outliers

Bioconductor version: Development (3.22)

A robust and outlier-aware method for testing differences in cell-type proportion in 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 "4.5") 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")

Details biocViews Bayesian, DifferentialExpression, FlowCytometry, Metagenomics, Regression, SingleCell, Software, Spatial Version 2.1.10 In Bioconductor since BioC 3.15 (R-4.2) (3 years) License GPL-3 Depends R (>= 4.3.0) Imports instantiate (>= 0.2.3), stats, SingleCellExperiment, parallel, dplyr, tidyr, purrr, magrittr, rlang, tibble, boot, lifecycle, tidyselect, utils, ggplot2, ggrepel, patchwork, forcats, readr, scales, stringr, glue, crayon, cli, fansi System Requirements CmdStan (https://mc-stan.org/users/interfaces/cmdstan) URL https://github.com/MangiolaLaboratory/sccomp Bug Reports https://github.com/MangiolaLaboratory/sccomp/issues See More Suggests knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), markdown, loo, prettydoc, SeuratObject, tidyseurat, tidySingleCellExperiment, bayesplot, posterior 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.

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