bioinformatics

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics analysis.

Genome size estimation from long read overlaps

AI-powered IDE for bioinformatics — built by biologists, for biologists

Package for processing and analyzing glycans and their role in biology.

A program for assessing the T2T genome continuity and completeness

A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences

The software behind Chai's open-source Real-Time PCR instrument

Prediction of key transcription factors in cell fate determination using enhancer networks. See full ANANSE documentation for detailed installation in...

Genome inference from a population reference graph

Identification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement

🌈Scaffold genome sequence assemblies using linked or long read sequencing data

Bioinformatics tool to find integrons in bacterial genomes

Intuitive guide to multi-omics integration with toy examples: supervised latent components (DIABLO), unsupervised shared/partial/unique structure (DIV...

A DNA Sequence Alignment/Map (SAM) library for Clojure

🧬High-performance genetics- and genomics-related data visualization using Makie.jl

A tool for drawing ANI clustermap between all-vs-all microbial genomes

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

Search ClinicalTrials.gov trials, retrieve study details and results, and match patients to eligible trials via MCP. STDIO or Streamable HTTP.

Inference of microbial interaction networks from large-scale heterogeneous abundance data

Write reproducible code for getting and processing ChEMBL

Spatial-Linked Alignment Tool

Simple pileup-based variant caller

:snake: Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.

Tools for manipulating annotated data matrices

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

Robust and efficient workflows using a simple language agnostic approach

BBTools: Official suite of fast, multithreaded bioinformatics tools for DNA/RNA analysis. BBMap aligner, BBDuk trimmer, BBMerge, and 90+ other tools....

just annotate it, dammit!

Collection of cloud-based biomedical data science learning modules funded by the National Institute of General Medical Sciences at the NIH

SIB course on single cell transcriptomics by mostly using the Seurat pipeline

Calculation of interatomic interactions in molecular structures

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

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

Portable command-line tool to query bioinformatics APIs, data, databases and files.

Race and ethnicity Imputation from Disease history with Deep LEarning

Deep Learning based cell composition analysis with Scaden.

[Bioinformatics 2021] This is the repo for the paper `SumGNN: Multi-typed Drug Interaction Prediction via Efficient Knowledge Graph Summarization'.

Infectious Disease Sequencing Platform

Provide R access to the NCI Genomic Data Commons portal.

Differential analysis tool for coding-free researchers – instant statistical results and charts, ready for your lab meeting. Just unzip and run! No-co...

Massively parallel phylogenetic placement of genetic sequences

Blender plugin to process biological data and molecular work.

TypeDB Bio: Biomedical Knowledge Graph

tiara – a tool for DNA sequence classification

vcfdist: Accurately benchmarking phased variant calls

biotoolsregistry: discovery portal for bioinformatics software and databases

GEne Cluster prediction with COnditional random fields.