PyPI Stats
  • Insights
  • PyPI
  • GitHub
  • Search
  • Compare
  • Advisories
  • Ecosystem
  • About
Home

Search Packages

Find Python packages by name, description, GitHub topic, or filter by metrics
snakemake
snakemake

This is the development home of the workflow management system Snakemake. For general information, see

254K 3K 639
LUMC
pytest-workflow

Configure workflow/pipeline tests using yaml files.

57K 69 10
snakemake
snakefmt

The uncompromising Snakemake code formatter

28K 189 31
4dn-dcic
tibanna

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

13K 72 28
sequana
sequana

Sequana: a set of Snakemake NGS pipelines

6K 151 27
khanlab
snakebids

Snakemake + BIDS

2K 22 16
sequana
sequana-fastqc

sequana pipeline to perform parallel fastqc and summarize results with multiqc plot

2K 5 3
jfallmann
monsda

MONSDA, Modular Organizer of Nextflow and Snakemake driven hts Data Analysis

1K 12 3
dcdanko
moduleultra

A control center for complex bioinformatics pipelines

1K 1 1
OpenOmics
snakevision

A tool to visualize Snakemake workflows.

833 32 1
snakemake
snakedeploy

deploy a snakemake pipeline directly from version control (under development)

802 25 13
solida-core
solida

SOLIDA is command-line solution that facilitate the reproducibility and portability of NGS pipelines. It can easily organize the deployment, the data management and the execution of a Snakemake based workflow.

722 6 1
snek5000
snek5000

:snake: Python framework for Nek5000 :rocket:

699 31 11
pypsa
snakemake-storage-plugin-lfs

PyPSA-Eur: A Sector-Coupled Open Optimisation Model of the European Energy System

678 567 411
Bishop-Laboratory
rlpipes

A standardized R-loop-mapping pipeline

578 3 1
shandley
hecatomb

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data

578 60 13
Daylily-Informatics
snakemake-executor-plugin-pcluster-slurm

slurm executor for use by snakemake when running on the slurm flavor which is unique to aws parallel cluster slrum pcluster.

575 1 0
sunbeam-labs
sunbeamlib

A snakemake utility for metagenomic sequencing analysis

453 175 44
pnnl
pnnl-atlas

ATLAS - Three commands to start analyzing your metagenome data

419 404 98
smutch
snakedoc

A Sphinx extension for Snakemake workflows

412 9 1
metagenome-atlas
metagenome-atlas

ATLAS - workflows for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data.

388 404 98
jakelever
pubrunner

A framework for keeping biomedical text mining result up-to-date

384 42 6
epruesse
ymp

Flexible multi-omic pipeline system

365 17 4
pypsa
snakemake-storage-plugin-cached-http

PyPSA-Eur: A Sector-Coupled Open Optimisation Model of the European Energy System

351 567 411
    • Data from PyPI, GitHub, ClickHouse, and BigQuery