bioinformatics
Repositories (1488)
Cute tricks for SIMD vectorized binary encoding and decoding of nucleotides, in Rust.
A universal infrastructure layer for generative biology
An app store for scientific workflows, tools, notebooks, and services
A bioinformatic toolkit to align genome assemblies into pangenome graphs
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
A tool for cell instance aware segmentation in densely packed 3D volumetric images
SquiggleKit: A toolkit for manipulating nanopore signal data
Solid Tumor Associative Modeling in Pathology
Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
BioT5 (EMNLP 2023) and BioT5+ (ACL 2024 Findings)
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
Evaluating genome assemblies
Explainability techniques for Graph Networks, applied to a synthetic dataset and an organic chemistry task. Code for the workshop paper "Explainabilit...
Get assembly statistics from FASTA and FASTQ files
Generate duplex/single consensus reads to reduce sequencing noises and remove duplications
An NGS read trimming tool that is specific, sensitive, and speedy. (production)
Single Cell Analysis Pipelines
Mining CRISPRs in Environmental Datasets
💊 AI Research Assistant for Accelerated Drug Discovery. 🦞
Fast genomics quality control tools for sequencing data, written in Rust.
Highly customizable, ambiguity-aware dotplots for visual sequence analyses
Physicochemical properties, indices and descriptors for amino-acid sequences.
A fast 23andMe DNA parser and inferrer for Python
:book::books:An introductory tutorial for BioJava
Bio4j abstract model and general entry point to the project
TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
MMseqs2 app to run on your workstation or servers
SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts...
Application of pan-genome for population
MOLGENIS - for scientific data: management, exploration, integration and analysis.
Indexing & querying large assembly graphs -- in space, no one can hear you miao!
整理常用的群体遗传学分析流程和脚本
Framework for building fast genomics web tools with WebAssembly and WebWorkers
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...
Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
Local version of the virus identification and analysis web server (tool set)
Detecting methylation using signal-level features from Nanopore sequencing reads
(Meta-)genome screening for functional and natural product gene sequences
A hybrid assembly and MAG recovery pipeline (and more!)
Toolkit for calling structural variants using short or long reads
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...
The bridge between the NCBI Gene Expression Omnibus and Bioconductor
tools for reading, writing, generating, merging, and remapping SNPs
: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/...
R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)
DEEPScreen: Virtual Screening with Deep Convolutional Neural Networks Using Compound Images
Dotplot large Genomes in an Interactive, Efficient and Simple way