Bioconductor – conclus

DOI: 10.18129/B9.bioc.conclus  


ScRNA-seq Workflow CONCLUS – From CONsensus CLUSters To A Meaningful CONCLUSion

Bioconductor version: Release (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>

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biocViews ATACSeq, Classification, Clustering, Sequencing, SingleCell, Software, Technology
Version 1.0.0
In Bioconductor since BioC 3.13 (R-4.1) (
License GPL-3
Depends R (>= 4.1)
Imports dbscan, fpc, factoextra, Biobase, BiocFileCache, parallel, doParallel, foreach, SummarizedExperiment, biomaRt, AnnotationDbi, methods, dplyr, scran, scater, pheatmap, ggplot2, gridExtra, SingleCellExperiment, stats, utils, scales, grDevices, graphics, Rtsne, GEOquery, clusterProfiler, stringr, tools
Suggests knitr, rmarkdown, BiocStyle, S4Vectors, matrixStats,,, dynamicTreeCut, testthat
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