conclus
This package is for version 3.14 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: 3.14
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>
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")| conclus | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, Classification, Clustering, Sequencing, SingleCell, Software, Technology |
| Version | 1.2.4 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3 years) |
| License | GPL-3 |
| Depends | R (>= 4.1) |
| 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, DT |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, BiocStyle, S4Vectors, matrixStats, dynamicTreeCut, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | conclus_1.2.4.tar.gz |
| Windows Binary | conclus_1.2.4.zip |
| macOS 10.13 (High Sierra) | conclus_1.2.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/conclus |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/conclus |
| Bioc Package Browser | https://code.bioconductor.org/browse/conclus/ |
| Package Short Url | https://bioconductor.org/packages/conclus/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.14 | Source Archive |