Releases: AllenCell/cvapipe_analysis
Releases · AllenCell/cvapipe_analysis
Code for the Nature Paper
This is the version of the code used to generate the figures from the Nature paper:
Viana, M. P., Chen, J., Knijnenburg, T. A., Vasan, R., Yan, C., Arakaki, J. E., ... & Rafelski, S. M. (2023). Integrated intracellular organization and its variations in human iPS cells. Nature, 613(7943), 345-354.
v0.0.1
What's Changed
- Param by @vianamp in #2
- Features by @vianamp in #3
- added a step to compute features by @ritvikvasan in #1
- address comments from reviewers by @vianamp in #6
- Aggregation by @vianamp in #8
- Added ability to run in parallel on slurm by @vianamp in #9
- Replacing dask with
srun
and concurrent. by @vianamp in #11 - Adjusted the general and cluster module to be more general by @vianamp in #12
- Slurm compatible distributed code by @vianamp in #15
- Configs from master by @vianamp in #10
- Stereotypy and concordance implementations by @vianamp in #18
- Custom input and more by @vianamp in #19
- Minor fixes by @vianamp in #20
- move subfolder to init by @ritvikvasan in #21
- Preprocessing step for variance dataset by @vianamp in #23
- Shapemode reads from preprocessing by @vianamp in #24
- Controller by @vianamp in #25
- Stereotypy using control and IO by @vianamp in #26
- Formatting by @vianamp in #27
- Add vscode folder to gitignore by @vianamp in #28
- increase precision when encoding path points as strings in pca scanning by @colobas in #29
- Small updates from master by @vianamp in #32
- Op corr by @vianamp in #33
- Norm contrast by @vianamp in #34
- Norm contrast by @vianamp in #35
- Notebooks initial commit by @vianamp in #36
- Update README by @alexferrante in #41
- add dependencies for notebooks by @alexferrante in #43
- add convenience functionality for distributed mode by @alexferrante in #44
- fix: step name not accessible to distributor class by @alexferrante in #45
- Other datasets by @vianamp in #46
New Contributors
- @ritvikvasan made their first contribution in #1
- @colobas made their first contribution in #29
- @alexferrante made their first contribution in #41
Full Changelog: https://github.com/AllenCell/cvapipe_analysis/commits/v0.0.1