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 hotmail.fr>

Citation (from within R,
enter citation("conclus")):

Installation

To install this package, start R (version
“4.1”) and enter:

if (!requireNamespace("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")

 

Details

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
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Suggests knitr, rmarkdown, BiocStyle, S4Vectors, matrixStats, org.Hs.eg.db, org.Mm.eg.db, dynamicTreeCut, testthat
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