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gitter-lab / SINGE

Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data
MIT License
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Finish renaming SCINGE to SINGE in files #39

Closed agitter closed 4 years ago

agitter commented 4 years ago

Closes #20

This pull request will remove all references to the SCINGE name in the code and files. We need to decide what do to about the reference files. Should these be updated?

Here are a few of the locations that still need to be updated: https://github.com/gitter-lab/SINGE/blob/ccdc52368eeaddd312e2d30bb1c09ec620933ee0/code/adjmatrix2edgelist.m#L22

https://github.com/gitter-lab/SINGE/blob/ccdc52368eeaddd312e2d30bb1c09ec620933ee0/code/SINGE_Aggregate.m#L36-L40

https://github.com/gitter-lab/SINGE/blob/ccdc52368eeaddd312e2d30bb1c09ec620933ee0/tests/compare_example_output.sh#L29-L30

https://github.com/gitter-lab/SINGE/blob/ccdc52368eeaddd312e2d30bb1c09ec620933ee0/tests/compare_example_output.sh#L40-L41

Also the header row in the reference SCINGE_Ranked_Edge_List.txt files.

agitter commented 4 years ago

@atuldeshpande can you please review the changes? If the tests pass, I believe this is ready to merge.

There are still SCINGE references in the Dockerfile, which I'll update after making the next release. They refer to the versioned compiled binaries.

atuldeshpande commented 4 years ago

These changes look good.