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

A faster lmm for GWAS. Supports GPU backend.

Feature extraction algorithm for genomic data

Protein structure comparison tools such as SSAP and SNAP

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

Compute N50/NG50 and auN/auNG

Structural variation caller using third generation sequencing

The BridgeDb Library source code

Dash for Julia - A Julia interface to the Dash ecosystem for creating analytic web applications in Julia. No JavaScript required.

ProtVec can be used in protein interaction predictions, structure prediction, and protein data visualization.

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.

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

Method to optimally select samples for validation and resequencing

Binomica Public Repository for Biological Parts

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

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

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

Numerical Encoding for Human Genetic Variants

Improving genome bins through the combination of different binning programs

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

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

📚 🔬 PIA - Protein Inference Algorithms

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

Ultrafast sequence typing and gene detection from NGS raw reads

Ploidy agnostic phasing pipeline and algorithm

A fast 23andMe DNA parser and inferrer for Python

Classify sequencing reads using MinHash.

Differentiable molecular simulation of proteins with a coarse-grained potential

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

View proteins and trajectories in the terminal

Single Cell Analysis Pipelines

CoRA Docs

JavaScript VisualizationTools

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

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

A Framework for Coalescent Simulation in R

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

WebGL Heatmap Viewer for Big Data and Bioinformatics

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

GNparser normalises scientific names and extracts their semantic elements.

Core BioPerl 1.x code

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

Haplotype VCF comparison tools

Read and write FASTQ and FASTA efficiently from Python

A curated list of Cheminformatics libraries and software.

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

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

cython + htslib == fast VCF and BCF processing

Genomics using open source tools, running on GCP or AWS

Strelka2 germline and somatic small variant caller

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

Quickly search, compare, and analyze genomic and metagenomic data sets.

🍺🔬 Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

Precision HLA typing from next-generation sequencing data

Examples of using deep learning in Bioinformatics

Remote protein homology detection suite.

Version 5 of the CAFE phylogenetics software

Fast hash function for DNA sequences