biology/py-pydeseq2 0.5.4 FreeBSD

Python implementation of the popular DESeq2 R package

System: FreeBSD
Repository: FreeBSD ports
Maintainer: [email protected]
Last update: 2026-10-08
Commit: 2414383046
License: MIT
Categories: biology, python

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.

In the other systems

The newest version among them is 0.5.4, as upstream numbers it.

System

Port

Version

Vulnerabilities

Status

Maintainer

Last update

FreeBSD

biology/py-pydeseq2

0.5.4 newest

none known

[email protected]

2026-10-08

HardenedBSD

biology/py-pydeseq2

0.5.4 newest

no data

[email protected]

GhostBSD

biology/py-pydeseq2

0.5.4 newest

no data

[email protected]

Version history 1

0.5.4 2026-08-28 7fbbfb679c

Upstream's version as each commit to the port's Makefile set it, or as this site first saw it in the system's packages; the tree's own revisions are not versions here.

Install

Binary package:

pkg install py312-pydeseq2

From the ports tree:

cd /usr/ports/biology/py-pydeseq2/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	py312-pydeseq2>0:biology/py-pydeseq2

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repository	aarch64	amd64	armv6	armv7	i386
FreeBSD:14:latest	-	0.5.4	-	0.5.2	0.5.4
FreeBSD:14:quarterly	-	0.5.4	n/a	0.5.2	0.5.4
FreeBSD:15:latest	-	0.5.4	n/a	0.5.2	0.5.2
FreeBSD:15:quarterly	-	0.5.4	n/a	n/a	n/a
FreeBSD:16:latest	-	-	n/a	n/a	n/a
FreeBSD:16:quarterly	n/a	n/a	n/a	n/a	n/a

Dependency graph

Ports that need it on the left, what it needs to run on the right; at most 8 of each. "Dependencies" below lists them all.

graph LR
  me["biology/py-pydeseq2"]
  me --> d0["archivers/brotli"]
  me --> d1["archivers/libdeflate"]
  me --> d2["archivers/liblz4"]
  me --> d3["archivers/py-brotli"]
  me --> d4["archivers/py-zopfli"]
  me --> d5["archivers/zopfli"]
  me --> d6["archivers/zstd"]
  me --> d7["converters/fribidi"]
  me -.-> dmore(["129 more"])
  classDef this fill:#ab2b28,color:#ffffff,stroke:#ab2b28
  class me this

Dependencies

As this port's Makefile names them.

Build 1

${PYTHON_PKGNAMEPREFIX}hatchling>0 : devel/py-hatchling

Runtime 7

${PYTHON_PKGNAMEPREFIX}anndata>=0.8.0 : devel/py-anndata
${PYTHON_PKGNAMEPREFIX}formulaic>=1.0.2 : math/py-formulaic
${PYTHON_PKGNAMEPREFIX}formulaic_contrasts>=0.2.0 : math/py-formulaic-contrasts
${PYTHON_PKGNAMEPREFIX}matplotlib>=3.6.2 : math/py-matplotlib
${PYTHON_PKGNAMEPREFIX}pandas>=1.4.0 : math/py-pandas
${PYTHON_PKGNAMEPREFIX}scikit-learn>=1.1.0 : science/py-scikit-learn
${PYTHON_PKGNAMEPREFIX}scipy>1.11.0 : science/py-scipy

The full lists below include those, and their dependencies in turn.

Build dependencies 19

Run dependencies 137

The first 100 are listed.

No port depends on this one.

Configuration

No options to configure.

USES: python
Service scripts: none

Files

distinfo 1

File

Size

SHA256

pydeseq2-0.5.4.tar.gz

790481

49d6f47840b5444ea2b69be7857c6c4e58f369066a0fb24bc52f7d3a62bbd92c

Master sites 1

PYPI

Commit history 2

Date Commit Credits Log message

2026-10-08

2414383046

Jason W. Bacon

Release numerous ports to ports@

I've been retired for a few years, and it is unlikely I will be doing any more scientific computing support in the future. I have continued to maintain ~160 ports to the best of my ability, mainly as a favor to the community, but I can no longer justify the time and effort required. I am therefore releasing most of my scientific ports, along with a few others, to ports@. I will continue to maintain ports I am actively using and those for which I am upstream.

2026-08-28

7fbbfb679c

Jason W. Bacon

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