A useful module for alligning cell lines to tumors
Project description
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
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
Project details
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