cahanlab/pysinglecellnet

singleCellNet in Python

PySingleCellNet: a computational toolkit for the single cell analysis and comparison of embryos and embryo models

PySingleCellNet (PySCN) predicts the 'cell type' of query scRNA-seq data by Random forest multi-class classification. See Tan & Cahan 2019 for more details. PySCN includes functionality to aid in the analysis of engineered cell populations (i.e. cells derived via directed differentiation of pluripotent stem cells or via direct conversion).

pysinglecellnet's Issues

any functions for viewing gene pairs

Hi! Are there any functions to visualize the top gene pairs? Or even in the variable xpairs, is it possible to identify which are the top genes associated with each of the dLevel's?

thanks!

Import repetition of sklearn in setup.py

In setup.py sklearn package is imported twice. This might sometimes cause errors when installing PySingleCellNet.

Error with pySCN.scn_classify: "Data matrix has wrong shape(), need to be (x,y)."

I've been using the same code that worked for me previously, but just started getting an error at the pySCN.scn_classify step and was wondering what I might be doing wrong or if there is an incompatibility with one of the package versions I am using. It throws an error when ad._core.views.ArrayView is called.

My code is below, as well as a screenshot of my error report and session info. Files are too large to be uploaded here but are in my Dropbox under Cahan lab: Kathleen.Noller/forgithub/ (https://www.dropbox.com/s/k5hrbbflh32w56x/forgithub.zip?dl=0)

adRaw = sc.read_loom("../data/LLi-21-FT/velocyto/LLi-21-FT.loom")
adRaw.obs_names_make_unique()
adRaw.var_names_make_unique()

from joblib import dump, load

tspRF = load("../101520/tspRF_FallopianTube_Ahmed_101520.joblib")
cgenesA = load("../101520/cgenesA_FallopianTube_Ahmed_101520.joblib")
xpairs = load("../101520/xpairs_FallopianTube_Ahmed_101520.joblib")

adClassRes = pySCN.scn_classify(adRaw, cgenesA, xpairs, tspRF, nrand = 0)

Thank you for your help!