bioinformatics

MyVariant.info: A BioThings API for human variant annotations

Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping

PacBio® variant and consensus caller

Same species annotation lift over pipeline.

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

My solution to Bioinformatics Specialization (Finding Hidden Messages in DNA; Genome Sequencing; Comparing Genes, Proteins, and Genomes; Molecular Evo...

ProtFlash: A lightweight protein language model

Compacted and colored de Bruijn graph construction and querying

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

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

Bring your single-cell data to life

Benchmark for LLM-based Agents in Computational Biology

Genome inference from a population reference graph

FastOMA is a scalable software package to infer orthology relationship.

A lightweight and high-performance bioinformatics package in Golang

Extensible specification for representing and uniquely identifying biological sequence variation

A package for designing compact and comprehensive capture probe sets.

A program for assessing the T2T genome continuity

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

Simple pileup-based variant caller

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

Rapid standardisation and quality control of GWAS or QTL summary statistics

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

Structural Quality Assessment for Biomolecular Structure Prediction Models

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

Software for predicting library complexity and genome coverage in high-throughput sequencing.

Command line utility for manipulating FASTQ files

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

Fast genomics quality control tools for sequencing data, written in Rust.

just annotate it, dammit!

Tools for manipulating annotated data matrices

Robust and efficient workflows using a simple language agnostic approach

Spatial-Linked Alignment Tool

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

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

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

Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome

Predict AMPs in (meta)genomes and peptides

Race and ethnicity Imputation from Disease history with Deep LEarning

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

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

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

Infectious Disease Sequencing Platform

Deep Learning based cell composition analysis with Scaden.

Provide R access to the NCI Genomic Data Commons portal.

Write reproducible code for getting and processing ChEMBL

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

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

Blender plugin to process biological data and molecular work.

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference