| Port details |
- py-pydeseq2 Python implementation of the popular DESeq2 R package
- 0.5.4 biology
 =0      0.5.2_2Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2025-06-11 14:27:03
- Last Update: 2026-08-28 12:12:42
- Commit Hash: 7fbbfb6
- Also Listed In: python
- License: MIT
- WWW:
- https://github.com/owkin/PyDESeq2
- Description:
- PyDESeq2 is a python implementation of the DESeq2 method for
differential expression analysis (DEA) with bulk RNA-seq data,
originally in R. It aims to facilitate DEA experiments for python
users.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - There is no configure plist information for this port.
- USE_RC_SUBR (Service Scripts)
- no SUBR information found for this port
- Dependency lines:
-
- ${PYTHON_PKGNAMEPREFIX}pydeseq2>0:biology/py-pydeseq2@${PY_FLAVOR}
- To install the port:
- cd /usr/ports/biology/py-pydeseq2/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/py-pydeseq2
- pkg install py312-pydeseq2
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
NOTE: This is a Python port. Instead of py312-pydeseq2 listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py312-pydeseq2
- Package flavors (<flavor>: <package>)
- distinfo:
- TIMESTAMP = 1787830075
SHA256 (pydeseq2-0.5.4.tar.gz) = 49d6f47840b5444ea2b69be7857c6c4e58f369066a0fb24bc52f7d3a62bbd92c
SIZE (pydeseq2-0.5.4.tar.gz) = 790481
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- py312-hatchling>0 : devel/py-hatchling@py312
- python3.12 : lang/python312
- py312-build>=0 : devel/py-build@py312
- py312-installer>=0 : devel/py-installer@py312
- Test dependencies:
-
- python3.12 : lang/python312
- Runtime dependencies:
-
- py312-anndata>=0.8.0 : devel/py-anndata@py312
- py312-formulaic>=1.0.2 : math/py-formulaic@py312
- py312-formulaic_contrasts>=0.2.0 : math/py-formulaic-contrasts@py312
- py312-matplotlib>=3.6.2 : math/py-matplotlib@py312
- py312-pandas>=1.4.0 : math/py-pandas@py312
- py312-scikit-learn>=1.1.0 : science/py-scikit-learn@py312
- py312-scipy>1.11.0 : science/py-scipy@py312
- python3.12 : lang/python312
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_py-pydeseq2
- USES:
- python
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 8
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
0.5.4
28 Aug 2026 12:12:42
 |
Jason W. Bacon (jwb) |
biology/py-pydeseq2: Update to 0.5.4
Drop support for python 3.10
Modernize build system
A few fixes and enhancements
Changes: https://github.com/scverse/PyDESeq2/releases
Reported by: portscout |
0.5.2_3
05 May 2026 19:29:37
|
Max Brazhnikov (makc) |
*/*: bump PORTREVISION after switching to NumPy 2.x |
0.5.2_2
05 May 2026 19:29:37
 |
Max Brazhnikov (makc) |
*/*: Switch to NumPy 2.x
PR: 294328
Exp-run: antoine |
0.5.2_2
03 Apr 2026 20:52:43
|
Charlie Li (vishwin) |
python.mk: retire ${PYNUMPY}
With both math/py-numpy (2) and math/py-numpy1, the variable stopped
making sense. Also remove the upper version bound. |
0.5.2_2
03 Apr 2026 18:52:22
|
Charlie Li (vishwin) |
math/py-numpy: switch all consumers to math/py-numpy1
...and bump PORTREVISIONs of consumers with hard RUN_DEPENDS
PR: 281470 |
0.5.2_1
31 Aug 2025 10:30:51
|
Rene Ladan (rene) |
all: bump PORTREVISION after updating graphics/libyuv
Using the Tools/scripts/bump_revision.pl script |
0.5.2
28 Jun 2025 11:45:57
|
Jason W. Bacon (jwb) |
biology/py-pydeseq2: Update to 0.5.2
Minor code cleanup
Changes: https://github.com/owkin/PyDESeq2/releases/tag/v0.5.2
Reported by: portscout |
0.5.1
11 Jun 2025 14:24:15
|
Jason W. Bacon (jwb) |
biology/py-pydeseq2: Python reimplementation of the DESeq2 R package
PyDESeq2 is a python implementation of the DESeq2 method for
differential expression analysis (DEA) with bulk RNA-seq data,
originally in R. It aims to facilitate DEA experiments for python
users. |
Number of commits found: 8
|
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