398 Open source projects that are alternatives of or similar to Ragoo

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

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

Bio4j abstract model and general entry point to the project

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

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

API for linked biological knowledge

A fast whole-genome aligner based on de Bruijn graphs

Golang for Bioinformatics

Unix, R and python tools for genomics and data science

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

BioGrakn Knowledge Graph

Open source Java library for computational proteomics

List of Computer Science courses with video lectures.

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.

Provides access to complex Bioinformatics software (even BioLinux!) in just one command.

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

Scripts to download genomes from the NCBI FTP servers

Improving genome bins through the combination of different binning programs

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

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

BWK awk modified for biological data

Classify sequencing reads using MinHash.

Robust and efficient workflows using a simple language agnostic approach

Single Cell Analysis Pipelines

Tools to process and analyze deep sequencing data.

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

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

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

MMseqs2: ultra fast and sensitive search and clustering suite

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

Flexible genotype query among 30,000+ samples whole-genome

Genomics using open source tools, running on GCP or AWS

d3 library to build circular graphs

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

Python module for average nucleotide identity analyses

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

Bioinformatics containers

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

😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎

A faster lmm for GWAS. Supports GPU backend.

Tools for working with SAM/BAM data

Structural variation caller using third generation sequencing

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

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

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

JavaScript VisualizationTools

compacted de Bruijn graph construction in low memory

Core BioPerl 1.x code

A fast and sensitive gapped read aligner

Strelka2 germline and somatic small variant caller

Pegasus Workflow Management System - Automate, recover, and debug scientific computations.

Plant image analysis using OpenCV

The sources of the openSNP website

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

R package for analyzing single-cell RNA-seq data

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

Application for making ENCODE Blacklists

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

UNCURL is a tool for single cell RNA-seq data analysis.

Introduction to the Unix Shell for biologists