459 Open source projects that are alternatives of or similar to orfipy

Official git repository for Biopython (originally converted from CVS)

A curated list of awesome bioinformatics software.

waka waka

Python and C++ code for reading and writing genomics data.

Efficient pythonic random access to fasta subsequences

A fast 23andMe genome text file parser, now superseded by arv

A package for designing compact and comprehensive capture probe sets.

UGENE is free open-source cross-platform bioinformatics software

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

Analysis pipelines for sequencing data

Data intensive science for everyone.

A collection of scripts and notes related to genomics and bioinformatics

Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

Official code repository for GATK versions 4 and up

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Simple pure Python SAM parser and objects for working with SAM records

A Kotlin DSL and library to create and plot RNA 2D structures

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

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

MView extracts and reformats the results of a sequence database search or multiple alignment.

🎯 Human transcription factor target genes.

Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)

Golang for Bioinformatics

Feature extraction algorithm for genomic data

Compute N50/NG50 and auN/auNG

Open source Java library for computational proteomics

ProteinGCN: Protein model quality assessment using Graph Convolutional Networks

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.

Method to optimally select samples for validation and resequencing

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources

Streamlining SLAM-seq analysis with ultra-high sensitivity

Improving genome bins through the combination of different binning programs

🐛 How to use CENTIPEDE to determine if a transcription factor is bound.

A python wrapper for the benchling api

An R package for reproducible and automated ADMIXTOOLS analyses

📊 Codon usage tables in code-friendly format + Python bindings

Ploidy agnostic phasing pipeline and algorithm

pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/

Classify sequencing reads using MinHash.

An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data.

Mulled - Automatized Containerized Software Repository

VSCode Extension for interactively visualising protein structure data in the editor

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

Single Cell Analysis Pipelines

GRAph-based Finding of Individual Motif Occurrences

A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.

A curated list of resources for machine learning for small-molecule drug discovery

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

dysgu-SV is a collection of tools for calling structural variants using short or long reads

Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).

Read and write FASTQ and FASTA efficiently from Python

The BridgeDb Library source code

A permissively licensed library designed to replace Illumina's Experiment Manager