This repository contains analysis code accompanying the paper

Sarkar, A. and Stephens, M. ”Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis.” Nature Genetics (2021).

The minimal specification of the working environment is

xargs -L100 conda create -n scmodes -c aksarkar <<EOF
bokeh
colorcet
ipython
jedi=0.17.1
jupyter_console
matplotlib=3.0.3
numpy
pandas
pytest
python=3.6.9=h265db76_0
pytorch
r-ashr=2.2.51.dev1
r-base=3.5.1
r-descend
r-devtools
r-expint
r-invgamma
r-irlba
r-mixsqp=0.3.45.dev1
r-roxygen2
r-testthat
scikit-learn
scipy
scqtl
EOF

source activate scmodes
xargs -L100 python -m pip install <<EOF
-e /project2/mstephens/aksarkar/projects/scmodes/
git+https://github.com/aksarkar/wlra.git#egg=wlra
h5py==2.10.0
rpy2==3.2.4
scanpy==1.5.1
EOF

We need to mix pip and conda due to incompatibilities in the biopython build of scanpy.