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dev-python/pyaml-env

Parse YAML configuration with environment variables in Python

dev-python/pybedtools

Use BED and GFF files from python using BEDtools

dev-python/pyct

Python packaging Common Tasks

dev-python/pyfaidx

Efficient pythonic random access to fasta subsequences

dev-python/pynndescent

Fast approximate nearest-neighbour search via Nearest-Neighbour Descent

dev-python/pynwb

A Python API for working with Neurodata stored in the NWB Format

dev-python/pysolar

Collection of Python libraries for simulating the irradiation by the sun

dev-python/python-gantt

Draw Gantt charts from Python

dev-python/reretry

An easy-to-use but functional retry decorator in python

dev-python/pyzo

The Python IDE for scientific computing

dev-python/ripser

python frontend for the fast ripser tda tool

dev-python/snakemake

Make-like task language

dev-python/snakemake-interface-common

Common functions and classes for Snakemake and its plugins

dev-python/snakemake-interface-executor-plugins

Stable interface for interactions between Snakemake and its executor plugins

dev-python/snakemake-interface-logger-plugins

Snakemake Logger Plugin Interface

dev-python/snakemake-interface-report-plugins

The interface for Snakemake report plugins

dev-python/snakemake-interface-storage-plugins

Stable interface for interactions between Snakemake and its storage plugins

dev-python/spectra

Easy color scales and color conversion for Python

dev-python/spikeinterface

A Python-based module for creating flexible and robust spike sorting pipelines.

dev-python/texext

Sphinx extensions for working with LaTeX math

dev-python/transforms3d

Functions for 3D coordinate transformations

dev-python/throttler

Easy throttling with asyncio support

dev-python/uhi

Universal Histogram Interface

dev-python/umap-learn

Uniform Manifold Approximation and Projection: fast non-linear dimension reduction

dev-python/visvis

An object oriented approach to visualization of 1D to 4D data

dev-python/wirerope

A wrapper interface for python callables

dev-python/wraps

Meaningful and safe wrapping types.

dev-python/xopen

Open compressed files transparently

dev-python/yte

A YAML template engine with Python expressions

dev-python/zarr_checksum

Calculatine zarr checksums from local or cloud storage

dev-util/makefile2graph

Create a graph of dependencies from GNU Make

dev-vcs/dandi-cli

DANDI command line client to facilitate common operations

dev-vcs/datalad

Keep code, data, containers under control with git and git-annex

dev-vcs/datalad-fuse

Keep code, data, containers under control with git and git-annex

media-libs/imglib2

A multidimensional, type-agnostic image processing library.

sci-biology/exonerate-gff3

exonerate-2.2.0 with patches to add GFF3 formatted output

sci-biology/GAL

Genome Annotation Library (incl. fasta_tool)

sci-biology/BEP032tools

Conversion and validation tools for BEP 032

sci-biology/Fastaq

Manipulate FASTA/Q, GFF3, EMBL, GBK files with API for developers

sci-biology/afni

Analysis of Functional Neuroimages by NIMH

sci-biology/bambus

Scaffolding Polymorphic Genomes and Metagenomes, a part of AMOS bundle

sci-biology/brkraw

Fast and easy statistical learning on NeuroImaging data

sci-biology/bx-python

Library for rapid implementation of genome scale analyses

sci-biology/cutadapt

Adapter trimming and other preprocessing of high-throughput sequencing reads

sci-biology/dcmstack

DICOM to Nifti coversion

sci-biology/deeptools

Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig

sci-biology/dipy

Computational neuroanatomy project focusing on diffusion MRI

sci-biology/gffutils

GFF and GTF file manipulation and interconversion

sci-biology/jtreeview-bin

Viewer for Microarray Data in PCL or CDT formats

sci-biology/multiqc

Aggregate bioinformatics results across many samples into a single report