recipe bioconductor-conclus

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

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/conclus.html

License:

GPL-3

Recipe:

/bioconductor-conclus/meta.yaml

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

Versions:

1.5.0-0,  1.2.0-0,  1.0.0-0

Depends:

• bioconductor-annotationdbi >=1.60.0,<1.61.0

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-biocfilecache >=2.6.0,<2.7.0

• bioconductor-biomart >=2.54.0,<2.55.0

• bioconductor-clusterprofiler >=4.6.0,<4.7.0

• bioconductor-geoquery >=2.66.0,<2.67.0

• bioconductor-org.hs.eg.db >=3.16.0,<3.17.0

• bioconductor-org.mm.eg.db >=3.16.0,<3.17.0

• bioconductor-scater >=1.26.0,<1.27.0

• bioconductor-scran >=1.26.0,<1.27.0

• bioconductor-singlecellexperiment >=1.20.0,<1.21.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-dbscan

• r-doparallel

• r-dplyr

• r-factoextra

• r-foreach

• r-fpc

• r-ggplot2

• r-gridextra

• r-pheatmap

• r-rlang

• r-rtsne

• r-scales

• r-stringr

Required By:

Installation

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 quay.io/biocontainers/bioconductor-conclus:<tag>

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

Download stats

Link to this page

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