Celligner

celligner is a computational project to align multiple cancer datasets across sequencing modalities, tissue conditions (media, perturbations..) and format (CL/tumor/organoids/spheroids)

see our latest paper on aligning CCLE cell lines with TCGA tumors: 2020 paper

Install

TO see the old R package installation instruction, see the R/folder.

pip install celligner

a dockerized version is available at jkobject:pycelligner

for developers

see CONTRIBUTING.md

run Celligner

see docs/Celligner_demo.[html|pdf] for an example of usage.

Multidataset alignment

see docs/Celligner_demo.[html|pdf] for an example of usage.

one can use addToFit(), addToPredict() depending on whether they want to align their dataset to another or align another dataset to theirs.

if you have a very small dataset and want to align to CCLE or CGA, use the parameter doAdd=True in order to not rerun the entire pipeline and use cached information.

R celligner

for the original R version of celligner, please check the R/README.md file here: https://github.com/broadinstitute.org/celligner/tree/master/R/README.md

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Please use github issues for any problem related to the tool.

Maintainers:

Jérémie Kalfon @jkobject James McFarland Javad Noorbak @jnoorbak

Created by:

Allie Warren @awarren