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

1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates

Fast Reference-Guided Scaffolding of Genome Assembly Contigs. RagTag, the successor to RaGOO, is now available here: https://github.com/malonge/RagTag

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.

Unix, R and python tools for genomics and data science

Bioconductor cheat sheet

List of Computer Science courses with video lectures.

G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST.

Scripts to download genomes from the NCBI FTP servers

BioGrakn Knowledge Graph

BWK awk modified for biological data

Method to optimally select samples for validation and resequencing

Tools to process and analyze deep sequencing data.

MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.

MMseqs2: ultra fast and sensitive search and clustering suite

Binomica Public Repository for Biological Parts

d3 library to build circular graphs

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Bioinformatics containers

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

Tools for working with SAM/BAM data

A curated list of bioinformatics bench-marking papers and resources.

Python library to facilitate genome assembly, annotation, and comparative genomics

Pytorch/Python3 implementation of DeepAccNet, protein model accuracy evaluator.

A fast and sensitive gapped read aligner

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Plant image analysis using OpenCV

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

Ultra-fast and memory-efficient (meta-)genome assembler

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

A scikit-learn compatible library for graph kernels

Numerical Encoding for Human Genetic Variants

Open-source bioinformatics components for Dash

Bayesian haplotype-based mutation calling

Interactive network visualization in Python and Dash, powered by Cytoscape.js

Improving genome bins through the combination of different binning programs

A library for generating an interactive SVG visualization of CWL workflows

A comprehensive library for computational molecular biology

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

Therapeutics Data Commons: Machine Learning Datasets and Tasks for Therapeutics

Fast multi-line FASTA/Q reader in several programming languages

Accurate sample inference from amplicon data with single nucleotide resolution

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

An analysis and visualization platform for 'omics data

COBRApy is a package for constraint-based modeling of metabolic networks.

📚 🔬 PIA - Protein Inference Algorithms

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315

annotate a VCF with other VCFs/BEDs/tabixed files

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

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

Python Programming for Biologists

Support Vector Structural Variation Genotyper

Bystro genetic analysis (annotation, filtering, statistics)

A Python platform for Structural Bioinformatics

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

Computational Analysis of Novel Drug Opportunities