Cluster Alignment Tool (CAT)

Installation

$ pip install cat-python

Installation from source

$ pip install git+https://github.com/brickmanlab/cat-python.git@master

Running CAT

$ catcli \
    --ds1 ./tests/datasets/mock.h5ad \
    --ds1_name DS1 \
    --ds1_cluster Condition_E+D \
    --ds2 ./tests/datasets/mock.h5ad \
    --ds2_name DS2 \
    --ds2_cluster Condition_E+D \
    --output ./res

Build documentation

$ sphinx-build -M html docs docs/_build

Citation

Please consider citing scANVI Explainer if you use in your research.

Rothová, M.M., Nielsen, A.V., Proks, M. et al.
Identification of the central intermediate in the extra-embryonic to embryonic endoderm transition through single-cell transcriptomics.
Nat Cell Biol 24, 833–844 (2022). 10.1038/s41556-022-00923-x

@article{rothova2022,
  title = {Identification of the Central Intermediate in the Extra-Embryonic to Embryonic Endoderm Transition through Single-Cell Transcriptomics},
  author = {Rothov{\'a}, Michaela Mrugala and Nielsen, Alexander Valentin and Proks, Martin and Wong, Yan Fung and Riveiro, Alba Redo and {Linneberg-Agerholm}, Madeleine and David, Eyal and Amit, Ido and Trusina, Ala and Brickman, Joshua Mark},
  year = {2022},
  month = jun,
  journal = {Nature Cell Biology},
  volume = {24},
  number = {6},
  pages = {833--844},
  publisher = {Nature Publishing Group},
  issn = {1476-4679},
  doi = {10.1038/s41556-022-00923-x}
}