conclus

DOI: 10.18129/B9.bioc.conclus    

This package is for version 3.15 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: 3.15

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 <rachedi.ilyess at gmail.com>

Installation

To install this package, start R (version "4.2") 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")

 

PDF	R Script	conclus
PDF		Reference Manual
Text		NEWS

Details

biocViews	ATACSeq, Classification, Clustering, Sequencing, SingleCell, Software, Technology
Version	1.3.3
In Bioconductor since	BioC 3.13 (R-4.1) (1.5 years)
License	GPL-3
Depends	R (>= 4.2)
Imports	org.Hs.eg.db, org.Mm.eg.db, 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, rlang
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, S4Vectors, matrixStats, dynamicTreeCut, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	conclus_1.3.3.tar.gz
Windows Binary
macOS Binary (x86_64)	conclus_1.3.3.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/
Package Downloads Report	Download Stats