pormr / RankCorr

A marker selection method for scRNA-seq data based on rank correlation

RankCorr

A marker selection method for scRNA-seq data based on rank correlation. See the notebook RankCorr-example.ipynb for a full walkthough of how to run the method; an outline is presented below.

The RankCorr method is contained in a highly modified version of the PicturedRocks data analysis package.
The modified version is included here. See the PicturedRocks repository for further information and extra (new) tools!

from picturedRocks import Rocks

Required inputs for the Rocks class:

• X, an np.ndarry of gene counts. Each row should contain the genetic information from a cell; the columns of X correspond to the genes (note that this is the transpose of some commonly used packages).
• y, a vector of cluster labels. These labels must be consecutive integers starting at 0.

data = Rocks(X, y)

lamb = 2.0 # the sparsity parameter
markers = data.CSrankMarkers(lamb=lamb)