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

List of Computer Science courses with video lectures.

Golang for Bioinformatics

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

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

Scripts to download genomes from the NCBI FTP servers

Open source Java library for computational proteomics

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

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.

BWK awk modified for biological data

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

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

Improving genome bins through the combination of different binning programs

Tools to process and analyze deep sequencing data.

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

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

Classify sequencing reads using MinHash.

MMseqs2: ultra fast and sensitive search and clustering suite

Single Cell Analysis Pipelines

SortMeRNA: next-generation sequence filtering and alignment tool

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

d3 library to build circular graphs

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

compacted de Bruijn graph construction in low memory

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

Bioinformatics containers

Genomics using open source tools, running on GCP or AWS

ECG classification programs based on ML/DL methods

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

Tools for working with SAM/BAM data

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

🌈Scaffold genome sequence assemblies using linked read sequencing data

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

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

A faster lmm for GWAS. Supports GPU backend.

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

Structural variation caller using third generation sequencing

A fast and sensitive gapped read aligner

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

Genome inference from a population reference graph

JavaScript VisualizationTools

Plant image analysis using OpenCV

Core BioPerl 1.x code

Bayesian haplotype-based mutation calling

Strelka2 germline and somatic small variant caller

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

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

LAMBDA – the Local Aligner for Massive Biological DatA

Examples of using deep learning in Bioinformatics

A scikit-learn compatible library for graph kernels

Analytical Web Apps for Python, R, Julia, and Jupyter. No JavaScript Required.

pymzML - an interface between Python and mzML Mass spectrometry Files

Open-source bioinformatics components for Dash

R package for analyzing single-cell RNA-seq data

Package for fetching metadata and downloading data from SRA/ENA/GEO

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

Simple simulation of single-cell RNA sequencing data

An efficient FASTQ manipulation suite

Structural variant toolkit for VCFs

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

exploratory and interactive microbiome analyses based on heatmaps