bioinformatics

R package for the analysis of massive SNP arrays.

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

Fast alignment and preprocessing of chromatin profiles

Application and Python module for average nucleotide identity analyses of microbes.

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

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

Terminal protein structure viewer — interactive 3D visualization of PDB/mmCIF structures with cartoon ribbons, braille rendering, and Sixel/Kitty grap...

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to colle...

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

CodonTransformer (2M+ Downloads); The tool for codon optimization, optimizing DNA for protein expression

Differential expression analysis for single-cell RNA-seq data.

Bioinformatics Workbook repository

课题组每周研讨会

Constructing a pangenome gene graph

Earl Grey: A fully automated TE curation and annotation pipeline

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferr...

MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics

Tutorials on machine learning, artificial intelligence, data science with math explanation and reusable code (in python and R)

Clustering scRNAseq by genotypes

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

A structural variation pipeline for short-read sequencing

🔬 Bioinformatics Notebook. Scripts for bioinformatics pipelines, with quick start guides for programs and video demonstrations.

PhysiCell: Scientist end users should use latest release! Developers please fork the development branch and submit PRs to the dev branch. Thanks!

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

Population-scale genotyping using pangenome graphs

CLI tool for flexible and fast adaptive sampling on ONT sequencers

A Python library for Gene–environment interaction analysis via deep learning

Work with bioinformatic files using Arrow, Polars, and/or DuckDB

Aligns short reads using dynamic seed size with strobemers

viral-ngs: command line tools and wrappers for processing raw viral genomic data

dna2vec: Consistent vector representations of variable-length k-mers

Compressing protein structures effectively with torsion angles

AWS for Bioinformatics Researchers

Bioconductor cheat sheet

Make Picrust2 Output Analysis and Visualization Easier

MSA(Multiple Sequence Alignment) visualization python package for sequence analysis

A visualization grammar and GPU-accelerated toolkit for genomic data

Genomic interval operations on Pandas DataFrames

The uncompromising Snakemake code formatter

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

chromatin Variability Across Regions (of the genome!)

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies

Antimicrobial Resistance Identification By Assembly

pymzML - an interface between Python and mzML Mass spectrometry Files

A modular, python-based framework for mass spectrometry. Powered by nbdev.

BioGrakn Knowledge Graph

Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes

🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) used by RNA CASP, RNA PUZZLES, and me ;-) docs @ http://rna-...

Predict the binding affinity of protein-protein complexes from structural data