600 Open source projects that are alternatives of or similar to Nucleus

The Microbiome Interpretable Temporal Rule Engine

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

Feature Annotation Location Description Ontology

Bioinformatics one liners from Ming Tang

A fast 23andMe DNA parser and inferrer for Python

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

simple viewer for variant call format using htslib

A simplified pipeline for ctDNA sequencing data analysis

GA4GH Variation Representation Python Implementation

📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

use the noise

Mulled - Automatized Containerized Software Repository

Understand DNA structure and how machine learning can be used to work with DNA sequence data.

De novo genome assembly and multisample variant calling

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

🚦 Run Picard on BAM files and collate 90 metrics into one file.

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

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

Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.

The BridgeDb Library source code

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data

Finds SNP sites from a multi-FASTA alignment file

The Ontology for Biomedical Investigations

CoRA Docs

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

Python library to handle Gene Ontology (GO) terms

Phage-Host Interaction Search Tool

WebGL Heatmap Viewer for Big Data and Bioinformatics

High-performance error correction for Illumina resequencing data

micca - MICrobial Community Analysis

Easy genetic ancestry predictions in Python

Version 5 of the CAFE phylogenetics software

Modular and universal bioinformatics

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

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGen…

GNparser normalises scientific names and extracts their semantic elements.

Feature extraction algorithm for genomic data

👁 Python library to plot DNA sequence features (e.g. from Genbank files)

NexusTK DAT Object Viewer

Genomics using open source tools, running on GCP or AWS

Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.

🎯 Human transcription factor target genes.

A Framework for Coalescent Simulation in R

BWK awk modified for biological data

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

A python wrapper for the benchling api

xHLA: Fast and accurate HLA typing from short read sequence data

No description or website provided.

waka waka

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

The Chemistry Development Kit

Precision HLA typing from next-generation sequencing data

C library for high-throughput sequencing data formats

Versatile open-source tool for microbiome analysis

Signal-level algorithms for MinION data

Introduction to the Unix Shell for biologists

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

CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies

Visualizing DNA Sequences via Javascript