402 Open source projects that are alternatives of or similar to mulled

Single Cell Analysis Pipelines

Genomics using open source tools, running on GCP or AWS

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

Menu bar macOS app for running rkt in a macOS hypervisor CoreOS VM.

A faster lmm for GWAS. Supports GPU backend.

Fast hash function for DNA sequences

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

A package for designing compact and comprehensive capture probe sets.

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

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

An R package for reproducible and automated ADMIXTOOLS analyses

Structural variation caller using third generation sequencing

Read and write FASTQ and FASTA efficiently from Python

Classify sequencing reads using MinHash.

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

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

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

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

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

R mased batch sequence downloader, with primer development and in silico evaluation capabilities

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

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

CLI to run Docker Compose file as pod on rkt with integrated service discovery using Consul - EOL

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

Improving genome bins through the combination of different binning programs

Haplotype VCF comparison tools

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

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

Version 5 of the CAFE phylogenetics software

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

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

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)

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

GRAph-based Finding of Individual Motif Occurrences

API for linked biological knowledge

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

Feature extraction algorithm for genomic data

The BridgeDb Library source code

Golang for Bioinformatics

GNparser normalises scientific names and extracts their semantic elements.

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

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

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

Toolkit for preparing genomes for submission to NCBI

🎯 Human transcription factor target genes.

Computational Analysis of Novel Drug Opportunities

Open source Java library for computational proteomics

The Ensembl Compara Perl API and SQL schema

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

A simple command-line tool to download data from Joint Genome Institute databases

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.

Think Dockerfile & docker-compose for rkt

Ploidy agnostic phasing pipeline and algorithm

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

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

Compute N50/NG50 and auN/auNG

WebGL Heatmap Viewer for Big Data and Bioinformatics

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

Streamlining SLAM-seq analysis with ultra-high sensitivity