bioinformatics
Repositories (1438)
R Package for Single-Cell Dataset Processing and Visualization
Genome annotation pipeline
Simple phylogenetic tree visualization python package for phylogenetic analysis
A software package for computing features of peptides and proteins
DeepSpot: Deep learning model for predicting spatial transcriptomics from H&E histopathology images. Supports spot-level (Visium) and single-cell (Xen...
Annotation of VCF variants with functional impact and from databases (executable+library)
Sequence alignment tools
Biomedical NLP Corpus or Datasets.
A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima
MCP server for the ClinicalTrials.gov v2 API. Search trials, retrieve study details and results, and match patients to eligible trials.
A fast 23andMe genome text file parser, now superseded by arv
Bioinformatics16: DeepChrome: Deep-learning for predicting gene expression from histone modifications
Simple pure Python SAM parser and objects for working with SAM records
simplified searching, fetching, and parsing records from NCBI using their E-utilities interface
Create regional association plots from GWAS or meta-analysis
Long-read splice alignment with high accuracy
An integrated visual environment for metabolic modeling methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynami...
Graph neural networks for molecular machine learning: Implemented and compatible with TensorFlow and Keras.
ARG normalization by mapping to the ARO ontology.
GenoTEX: An expert-curated benchmark for evaluating LLM agents on real-world gene expression analysis tasks. (MLCB 2025 Oral)
Portable solution to generate genome alignment chains using lastz
A Snakemake workflow and MrBiomics module for performing and visualizing differential analyses of NGS data powered by the R package limma.
A modern multiple sequence alignment browser - built for the terminal.
⛓ Correct misassemblies using linked AND long reads
PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
Code for design of diagnostic PCR primers, and metabarcoding markers.
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
A package to annotate protein sequences
PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
Platform for running comp bio applications on distributed compute and storage infrastructure
Minimum Information about any (X) Sequence” (MIxS) specification
📄文档：医学和生信笔记公众号“生信数据挖掘”合集
Unsupervised Deep Disentangled Representation of Single-Cell Omics
An easy-to-use Hi-C data processing software supporting distributed computation.
:books: Various bioinformatics tutorials
GA4GH Variation Representation Python Implementation
A fully automated gene annotator from RNA-Seq expression data
生物信息学项目实践仓库🏆🥇
Allele-specific alignment sorting
A high-performance modification detection tool in Rust
A lightweight platform-accelerated library for biological motif scanning using position weight matrices.
Rust crates for working with Workflow Description Language (WDL) documents.
Docker for 4DN Hi-C processing pipeline
slurmR: A Lightweight Wrapper for Slurm
PDV: an integrative proteomics data viewer
Bioinformatics on GCP, AWS or Azure
Reference-based consensus creation
Deep learning-based tissue compositions and cell-type-specific gene expression analysis with tissue-adaptive autoencoder (TAPE)
Detection of remote homology by comparison of protein language model representations
Fast and accurate label-free quantification for small and very large numbers of proteomes