bioinformatics

Simple simulation of single-cell RNA sequencing data

PyChem-Pro: 100% Python API, fast, flexible & programmable molecular viewer - 2D and 3D, molecular docking pose viewer, cheminformatics library, molec...

A universal toolkit for upstream processing of long RNA reads

Nature Communications | BASALT (Binning Across a Series of Assemblies Toolkit) for binning and refinement of short- and long-read sequencing data

A collection of scripts and notes related to genomics and bioinformatics

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

Ten Quick Tips for Deep Learning in Biology

Fast alignment and preprocessing of chromatin profiles

:rocket: A sequencing simulator

:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics

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

R package for the analysis of massive SNP arrays.

Earl Grey: A fully automated TE curation and annotation pipeline

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

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

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

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

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

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

Clustering scRNAseq by genotypes

Bioinformatics Workbook repository

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

Constructing a pangenome gene graph

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

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

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

课题组每周研讨会

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

A structural variation pipeline for short-read sequencing

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

Fast indexing and search of discontinuous motifs in protein structures

Aligns short reads using dynamic seed size with strobemers

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

Population-scale genotyping using pangenome graphs

C-library for calculating Solvent Accessible Surface Areas

Make Picrust2 Output Analysis and Visualization Easier

CLI tool for flexible and fast adaptive sampling on ONT sequencers

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

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

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

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

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

Genomic interval operations on Pandas DataFrames

AWS for Bioinformatics Researchers

The uncompromising Snakemake code formatter

Compressing protein structures effectively with torsion angles

A visualization grammar and GPU-accelerated toolkit for genomic data

chromatin Variability Across Regions (of the genome!)