recipe bioconductor-conclus

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






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.

package bioconductor-conclus

(downloads) docker_bioconductor-conclus



Required By:


With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-conclus

and update with:

conda update bioconductor-conclus

or use the docker container:

docker pull<tag>

(see bioconductor-conclus/tags for valid values for <tag>)

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