Bioinformatics Analysis Python Packages

flowpaths

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

rnalysis

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

pyrsx

Rust RAD-seq marker analysis

buisciii-tools

set of helper tools for bu-isciii management of its core services portfolio.

phigaro

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

codonu

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

dohlee

My personal python utility library.

gmql

Python Library for data analysis based on GMQL

bidali

Biological Data Analysis Library

ciara-python

Implementation of entropy of mixing algorithm in python

pbxplore

PBxplore is a suite of tools dedicated to Protein Block analysis.

neticspy

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

pyrpipe

pyrpipe

kvasirhgt

Searching for Horizontal Gene Transfer

chronqc

Manuscript describing ChronQC is now available online in Bioinformatics

tcga-gdc-downloader

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

pistis

Quality control plotting for long reads

pyrice

PyRice: a Python package for functional analysis of rice genes

unifunc

Tool for similarity analysis of protein function annotations.

discere

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

pmoss

pMoSS (p-value Model using the Sample Size) is a Python code to model the p-value as an n-dependent function using Monte Carlo cross-validation. Exploits the dependence on the sample size to characterize the differences among groups of large datasets

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 library for parsing quality control information for the UMIs in 10x single cell gene expression assays