Bioinformatics Analysis Python Packages

rnalysis

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

flowpaths

A Python package to quickly decompose weighted graphs (acyclic or not) into weighted paths or walks, under various models.

buisciii-tools

Tools for managing and resolution of buisciii services.

phigaro

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

gmql

Python Library for data analysis based on GMQL

codonu

A python project for analysis of codon usage for gene or genome analysis

dohlee

:package: My personal python utility library.

bidali

Biological Data Analysis Library

pbxplore

A suite of tools to explore protein structures with Protein Blocks :snake:

ciara-python

Implementation of entropy of mixing algorithm in python

tcga-gdc-downloader

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

pyrpipe

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

kvasirhgt

A package to identify HGT in bacterial genomes

neticspy

Python implementation of NetICS. (Network-based Integration of Multi-omics data).

pistis

Quality control plotting for long reads

chronqc

Manuscript describing ChronQC is now available online in Bioinformatics

pyrice

PyRice is an API to access some Rice public databases at the same time with consistent output. PyRice design is modular and implements a smart query system which fits the computing resources to optimize the query speed.

unifunc

Tool for similarity analysis of protein function annotations.

pmoss

Python package to model the p-value as an n-dependent function using Monte Carlo cross-validation.

discere

Python code to extract features from Protein sequences for Machine Learning/Deep Learning

pyreqtl

A collection of Python modules equivalent to R ReQTL Toolkit aims to identify the association between expressed SNVs with their gene expression using RNA-sequencing data.

umiread

Lightweight utility for 10x single cell assays