recipe bioconductor-sincell

R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data



GPL (>= 2)




biotools: sincell

Cell differentiation processes are achieved through a continuum of hierarchical intermediate cell-states that might be captured by single-cell RNA seq. Existing computational approaches for the assessment of cell-state hierarchies from single-cell data might be formalized under a general workflow composed of i) a metric to assess cell-to-cell similarities (combined or not with a dimensionality reduction step), and ii) a graph-building algorithm (optionally making use of a cells-clustering step). Sincell R package implements a methodological toolbox allowing flexible workflows under such framework. Furthermore, Sincell contributes new algorithms to provide cell-state hierarchies with statistical support while accounting for stochastic factors in single-cell RNA seq. Graphical representations and functional association tests are provided to interpret hierarchies.

package bioconductor-sincell

(downloads) docker_bioconductor-sincell



Required By


With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-sincell

and update with:

conda update bioconductor-sincell

or use the docker container:

docker pull<tag>

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