netZoo / netZooPy

netZooPy is a network biology package implemented in Python.
https://netzoo.github.io/
GNU General Public License v3.0
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Changed visibility of compute_panda to public #313

Closed soelmicheletti closed 1 year ago

soelmicheletti commented 1 year ago

With the current implementation, it is possible to run PANDA only with the expression data. The internal implementation, however, uses co-expression. For some applications, it is useful to make the internal implementation public (e.g. if we investigate different co-expression correction methods).

codecov[bot] commented 1 year ago

Codecov Report

Patch coverage: 100.00% and project coverage change: +0.32% :tada:

Comparison is base (427070f) 57.52% compared to head (18cf61b) 57.84%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## devel #313 +/- ## ========================================== + Coverage 57.52% 57.84% +0.32% ========================================== Files 37 39 +2 Lines 2500 2519 +19 ========================================== + Hits 1438 1457 +19 Misses 1062 1062 ``` | [Files Changed](https://app.codecov.io/gh/netZoo/netZooPy/pull/313?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=netZoo) | Coverage Δ | | |---|---|---| | [netZooPy/cobra/\_\_init\_\_.py](https://app.codecov.io/gh/netZoo/netZooPy/pull/313?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=netZoo#diff-bmV0Wm9vUHkvY29icmEvX19pbml0X18ucHk=) | `100.00% <100.00%> (ø)` | | | [netZooPy/cobra/cobra.py](https://app.codecov.io/gh/netZoo/netZooPy/pull/313?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=netZoo#diff-bmV0Wm9vUHkvY29icmEvY29icmEucHk=) | `100.00% <100.00%> (ø)` | | | [netZooPy/panda/\_\_init\_\_.py](https://app.codecov.io/gh/netZoo/netZooPy/pull/313?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=netZoo#diff-bmV0Wm9vUHkvcGFuZGEvX19pbml0X18ucHk=) | `100.00% <100.00%> (ø)` | |

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soelmicheletti commented 1 year ago

And also COBRA in Python tested after the one in netZooR

marouenbg commented 1 year ago

@violafanfani can you have a final look and merge ?