PyPI Stats

Bioinformatics Pipeline Python Packages

Python packages with the GitHub topic bioinformatics-pipeline. Sorted by relevance, with stars and monthly downloads.
databio
piper

Python toolkit for building restartable pipelines

134K 47 9
milaboratory
polars-pf

PFrames - Python Polars extensions

17K 20 1
koszullab
hicstuff

Simple library/pipeline to generate and handle Hi-C data.

4K 39 8
GuyTeichman
rnalysis

Analyze your RNA sequencing data without writing a single line of code

3K 141 13
aureme
metage2metabo

From annotated genomes to metabolic screening in large scale microbiotas

2K 71 7
pepkit
looper

Modular job submitter for arbitrary pipelines or commands.

2K 26 7
bacalhau-project
bacalhau-apiclient

Community-driven, simple, yet powerful framework for fast, cost-effective distributed Compute over Data.

2K 858 100
bacalhau-project
bacalhau-sdk

Community-driven, simple, yet powerful framework for fast, cost-effective distributed Compute over Data.

1K 858 100
sanger-pathogens
ariba

ARIBA: Antibiotic Resistance Identification By Assembly

1K 187 60
genecell
piaso-tools

Precise Integrative Analysis of Single-cell Omics.

1K 6 2
LegumeFederation
lorax

a web server that "speaks for the (phylogenetic) trees"

1K 1 2
bobeobibo
phigaro

Phigaro is a scalable command-line tool for predicting phages and prophages

1K 52 15
nPhasePipeline
nphase

Ploidy agnostic phasing pipeline and algorithm

924 49 6
yodeng
runjob

runjob is a program for managing a group of related jobs running on a compute cluster

921 11 4
filecoin-project
bacalhau-airflow

Community-driven, simple, yet powerful framework for fast, cost-effective distributed Compute over Data.

907 858 100
ShujiaHuang
ilus

A lightweight and handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis by using GATK and Sentieon. 一个基于 GATK 和 Sentieon 的简易且全面的 WGS/WES 分析流程生成器.

891 143 36
DEIB-GECO
gmql

Python Library for data analysis based on GMQL

606 15 5
sanger-pathogens
circlator

A tool to circularize genome assemblies

471 255 57
RenneLab
hybkit

Toolkit for analysis of ".hyb" format nucleotide sequence data from chimeric RNA experiments.

339 8 1
sanger-pathogens
iva

Iterative Virus Assembler

316 58 19
gabrielvpina
viralquest

A user-friendly pipeline for viral diversity analysis and characterization.

299 13 1
onedimkurt
tcga-gdc-downloader

User-friendly tool to download TCGA STAR RNA-seq counts from the GDC portal

281 7 0
urmi-21
pyrpipe

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

272 86 29
niekwit
pycrispr

Pip package for CRISPR-Cas9 screen analysis

270 5 1