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Update rpy2 to pydeseq #19

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Update rpy2 to pydeseq #19

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97c7a4d
Updated function compute_diff_expression from limma (R) to pydeseq2 (…
CharlieNotChaplin Mar 23, 2026
d33a8cc
Fixed description for updated diff exp method.
CharlieNotChaplin Mar 23, 2026
50632ba
Added pydeseq2 to requirements
CharlieNotChaplin Mar 24, 2026
bdef79b
Fixed versioning for pydeseq2
CharlieNotChaplin Mar 24, 2026
98d6b1c
Added pydeseq function versions for original deseq2 functions
CharlieNotChaplin Mar 24, 2026
9b82c19
Updated functions to replace rpy2 with pydeseq. Fixed imports and doc…
CharlieNotChaplin Mar 31, 2026
1c25f85
Removed all old unused functions (mainly rpy2 based functions)
CharlieNotChaplin Mar 31, 2026
40e5f89
Relaxed version constraints in setup.py, updated README and cell_gene…
CharlieNotChaplin Apr 1, 2026
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6 changes: 2 additions & 4 deletions README.md
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Expand Up @@ -7,18 +7,17 @@ Although clinical applications represent the next challenge in single-cell genom
![plot](./img/plot.png)


Current version for PILOT is 2.0.6
Current version for PILOT is 2.0.7

## Installation
The easiest way to install PILOT and the required packages is using the following way:

```terminal
git clone https://github.com/CostaLab/PILOT.git
cd PILOT
conda create --name PILOT python=3.11.5 r-base
conda create --name PILOT python=3.14.3
conda activate PILOT
pip install .
conda install -c conda-forge rpy2
```
Once you've completed these steps, you can proceed to run the tutorials and explore the features of PILOT.
When doing so, remember to move to the tutorial folder, as all the work will be performed there:
Expand Down Expand Up @@ -52,4 +51,3 @@ You can access the used data sets by PILOT in Part 1 [![DOI](https://zenodo.org/




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