Top 704 bioinformatics open source projects

List of tools and resources related to the 10x Genomics GEMCode/Chromium system

SquiggleKit: A toolkit for manipulating nanopore signal data

EDAM is an ontology of bioinformatics types of data including identifiers, data formats, operations and topics.

GO enrichment with python -- pandas meets networkx

Bayesian genotyper for structural variants

MyGene.info: A BioThings API for gene annotations

Biological sequences for the julia language

A fast whole-genome aligner based on de Bruijn graphs

An interactive web tool for quality control of DNA sequencing data

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

Protein-Level ASSembler (PLASS): sensitive and precise protein assembler

Robust and efficient workflows using a simple language agnostic approach

The START App: R Shiny Transcriptome Analysis Resource Tool

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

Solutions to assignments of Coursera Specializations - Deep learning, Machine learning, Algorithms & Data Structures, Image Processing and Python For Everybody

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

Global Biotic Interactions provides access to existing species interaction datasets

compacted de Bruijn graph construction in low memory

Characterization of Germline variants

🌈Scaffold genome sequence assemblies using linked read sequencing data

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

Genome inference from a population reference graph

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

LAMBDA – the Local Aligner for Massive Biological DatA

A tutorial on methods of 16S analysis with QIIME 1

Model and predict short DNA sequence features with neural networks

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

A library for generating an interactive SVG visualization of CWL workflows

Python Programming for Biologists

Support Vector Structural Variation Genotyper

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

Yet Another Chimeric Read Detector

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Analysis pipelines for sequencing data

Lightweight Iterative Gene set Enrichment in R

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

Tools and databases for analyzing HLA and VDJ genes.

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

Official code repository for GATK versions 4 and up

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

Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image

Create regional association plots from GWAS or meta-analysis

Exact Tandem Repeat Finder (not a TRF replacement)

GeneValidator: Identify problems with predicted genes

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

MetaSRA: normalized sample-specific metadata for the Sequence Read Archive

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Comprehensive toolkit for generating various numerical features of protein sequences

R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data

Snakemake-based workflow for detecting structural variants in WGS data

Randomly subsample sequencing reads to a specified coverage

课题组每周研讨会

Seven Bridges API Client, CWL Schema, Meta Schema, and SDK Helper in R

A lightweight immune repertoire browser

A versatile pairwise aligner for genomic and spliced nucleotide sequences

A collection of publications on comparison of high-throughput sequencing technologies.

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

Single-Cell Analysis in Python. Scales to >1M cells.

A full spaCy pipeline and models for scientific/biomedical documents.

Estimate metagenomic coverage and sequence diversity