425 Open source projects that are alternatives of or similar to Awesome Cancer Variant Databases

Real-time species-typing visualisation for nanopore data.

Characterization of Germline variants

Single cell perturbation prediction

Aim to be the bioinformatics repository with more and newer packages

🌈Scaffold genome sequence assemblies using linked read sequencing data

This library tackles the construction and efficient execution of computational chemistry workflows

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests

Sample search by metadata and features

Parser and database to index the terpene profile of different strains of Cannabis from online databases

WebLogo 3: Sequence Logos redrawn

Application for making ENCODE Blacklists

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml

A tutorial on methods of 16S analysis with QIIME 1

The Microbiome Interpretable Temporal Rule Engine

Bioconductor cheat sheet

A simplified pipeline for ctDNA sequencing data analysis

1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates

Phylogenetic trees in Julia

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

Python Programming for Biologists

De novo assembly based variant calling pipeline for Illumina short reads

Toolset for SV simulation, comparison and filtering

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

Emperor a tool for the analysis and visualization of large microbial ecology datasets

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

NGLess: NGS with less work

Build and maintain multiple custom conda environments all in once place.

Yet Another Chimeric Read Detector

Earl Grey: A fully automated TE curation and annotation pipeline

BioGrakn Knowledge Graph

A fast 23andMe genome text file parser, now superseded by arv

Analysis pipelines for sequencing data

📊 Identify cell types and pathways affected by genetic risk loci.

A cool place to store your Hi-C

Project metadata manager for PEPs in Python

VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

transparently build CWL and Galaxy XML tool definitions for any script that uses argparse

Bio4j abstract model and general entry point to the project

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

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

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Introduction to the Unix Shell for biologists

MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.

Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)

Python package to annotate and visualize gene fusions.

Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝

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

A standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification and a web application for managing and executing those WES services.

Exact Tandem Repeat Finder (not a TRF replacement)

Proof-of-concept seq-to-graph mapper and graph generator

Intuitive local web frontend for the BLAST bioinformatics tool

RAxML Next Generation: faster, easier-to-use and more flexible

Python for Bioinformatics

The sources of the openSNP website

A tool to circularize genome assemblies