conclus

DOI: 10.18129/B9.bioc.conclus    

This package is for version 3.13 of Bioconductor; for the 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 (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")

 

PDF R Script conclus
PDF   Reference Manual
Text   NEWS

Details

biocViews ATACSeq, Classification, Clustering, Sequencing, SingleCell, Software, Technology
Version 1.0.0
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
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
LinkingTo
Suggests knitr, rmarkdown, BiocStyle, S4Vectors, matrixStats, org.Hs.eg.db, org.Mm.eg.db, dynamicTreeCut, testthat
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Enhances
URL
Depends On Me
Imports Me
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Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package conclus_1.0.0.tar.gz
Windows Binary conclus_1.0.0.zip
macOS 10.13 (High Sierra) conclus_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/conclus
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/conclus
Package Short Url https://bioconductor.org/packages/conclus/
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