bioinformatics

:book::books:An introductory tutorial for BioJava

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

整理常用的群体遗传学分析流程和脚本

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases...

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts...

Evaluating genome assemblies

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

Single Cell Analysis Pipelines

A Python package for CD-HIT, clustering protein or nucleotide sequences.

Framework for building fast genomics web tools with WebAssembly and WebWorkers

Solid Tumor Associative Modeling in Pathology

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

Detecting methylation using signal-level features from Nanopore sequencing reads

Indexing & querying large assembly graphs -- in space, no one can hear you miao!

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

Physicochemical properties, indices and descriptors for amino-acid sequences.

Application of pan-genome for population

Demonstrating best practices for bioinformatics command line tools

OWLTools

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells...

Toolkit for calling structural variants using short or long reads

DEEPScreen: Virtual Screening with Deep Convolutional Neural Networks Using Compound Images

tools for reading, writing, generating, merging, and remapping SNPs

Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package

Accurate and flexible loops calling tool for 3D genomic data.

Rapid Profiling and Deconvolution Tool for Metagenomes

FastQC port to Qt5: A quality control tool for high throughput sequence data.

:package: An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/...

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

CUT&RUN and CUT&Tag data processing and analysis

A Low-cost Open-source High-speed Multi-camera Motion Capture System.

Dotplot large Genomes in an Interactive, Efficient and Simple way

DashTools - Plotly Dash Command Line Tools - Create, Run and Deploy Templated Python Apps from Terminal

Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab

R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)

GNU-Make-like utility for managing builds and complex workflows

The bridge between the NCBI Gene Expression Omnibus and Bioconductor

This is the repo of the medical dialogue dataset 'imcs21' in CBLUE@Tianchi

Open source bioinformatics and computational biology toolbox written in F#. This is the core package containing type models and parsers/writers.

nucleosome calling using ATAC-seq

Python 3 library with good support for both reading and writing VCF

Sequence Indexing and Search

Rust bindings to minimap2 library

De novo assembly based variant calling pipeline for Illumina short reads

A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA

Simple FASTQ quality assessment using Python

my solutions to problems from Rosalind.

CCTyper: Automatic detection and subtyping of CRISPR-Cas operons

Affinity Protein-Protein Transformers—State of the art protein-protein binding affinity in seconds!