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conclus
This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see conclus.
ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion
Bioconductor version: 3.13
CONCLUS is a tool for robust clustering and positive marker features selection of single-cell RNA-seq (sc-RNA-seq) datasets. It takes advantage of a consensus clustering approach that greatly simplify sc-RNA-seq data analysis for the user. Of note, CONCLUS does not cover the preprocessing steps of sequencing files obtained following next-generation sequencing. CONCLUS is organized into the following steps: Generation of multiple t-SNE plots with a range of parameters including different selection of genes extracted from PCA. Use the Density-based spatial clustering of applications with noise (DBSCAN) algorithm for idenfication of clusters in each generated t-SNE plot. All DBSCAN results are combined into a cell similarity matrix. The cell similarity matrix is used to define "CONSENSUS" clusters conserved accross the previously defined clustering solutions. Identify marker genes for each concensus cluster.
Author: Ilyess Rachedi [cre], Nicolas Descostes [aut], Polina Pavlovich [aut], Christophe Lancrin [aut]
Maintainer: Ilyess Rachedi <ilyessr at hotmail.fr>
citation("conclus")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("conclus")
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("conclus")
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Follow Installation instructions to use this package in your R session.