recipe bioconductor-scate

SCATE: Single-cell ATAC-seq Signal Extraction and Enhancement






SCATE is a software tool for extracting and enhancing the sparse and discrete Single-cell ATAC-seq Signal. Single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) is the state-of-the-art technology for analyzing genome-wide regulatory landscapes in single cells. Single-cell ATAC-seq data are sparse and noisy, and analyzing such data is challenging. Existing computational methods cannot accurately reconstruct activities of individual cis-regulatory elements (CREs) in individual cells or rare cell subpopulations. SCATE was developed to adaptively integrate information from co-activated CREs, similar cells, and publicly available regulome data and substantially increase the accuracy for estimating activities of individual CREs. We demonstrate that SCATE can be used to better reconstruct the regulatory landscape of a heterogeneous sample.

package bioconductor-scate

(downloads) docker_bioconductor-scate



depends bioconductor-genomicalignments:


depends bioconductor-genomicranges:


depends bioconductor-preprocesscore:


depends bioconductor-scatedata:


depends r-base:


depends r-mclust:

depends r-rtsne:

depends r-splines2:

depends r-xgboost:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-scate

and update with::

   mamba update bioconductor-scate

To create a new environment, run:

mamba create --name myenvname bioconductor-scate

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-scate/tags`_ for valid values for ``<tag>``)

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