bioinformatics
Repositories (1472)
Horizontal gene transfer (HGT) identification pipeline
vembrane filters, sorts, and transforms VCF records using python expressions
Efficiently read and write sequencing data from Python
An integrated visual environment for metabolic modeling methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynami...
Fast FASTQ sample demultiplexing in Rust.
Nucleic Acids Research 2024：RNA-MSM model is an unsupervised RNA language model based on multiple sequences that outputs both embedding and attention...
Single-cell spatial omics analysis that makes you happy!
FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone...
CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology
A Python library to visualize and analyze long-read transcriptomes
Analysis of non-covalent interactions in MD trajectories
Elucidating the Utility of Genomic Elements with Neural Nets
RawHash can accurately and efficiently map raw nanopore signals to reference genomes of varying sizes (e.g., from viral to a human genomes) in real-ti...
Portable solution to generate genome alignment chains using lastz
Mulled - Automatized Containerized Software Repository
PDV: an integrative proteomics data viewer
Detecting methylation using signal-level features from Nanopore sequencing reads of plants
Collects software dedicated to predicting specific properties of peptides
ARG normalization by mapping to the ARO ontology.
SplitThreader has moved into Ribbon!
Annotation of VCF variants with functional impact and from databases (executable+library)
Protein structure comparison tools such as SSAP and SNAP
🏔 coverage extraction from BAM/CRAM files, supporting targets 📊
Teaching Material: Template Illustrating Components of an R package for BCB410H - Applied Bioinformatics (2019-2025), University of Toronto, Canada
MutMap pipeline to identify causative mutations responsible for a phenotype
(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia
Core library of the Genome Analysis Toolbox with de-Bruijn graph
API for linked biological knowledge
A geometric deep learning framework (Geometric Transformers) for predicting protein interface contacts. (ICLR 2022)
A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima
Python package to annotate and visualize gene fusions.
Genome annotation pipeline
Simple phylogenetic tree visualization python package for phylogenetic analysis
A software package for computing features of peptides and proteins
📄文档：医学和生信笔记公众号“生信数据挖掘”合集
The tool for in silico serotyping
Python interface for RCSB.org API services
Sequence alignment tools
Code for design of diagnostic PCR primers, and metabarcoding markers.
R Package for Single-Cell Dataset Processing and Visualization
生物信息学项目实践仓库🏆🥇
Graph neural networks for molecular machine learning: Implemented and compatible with TensorFlow and Keras.
Detection of remote homology by comparison of protein language model representations
QTL-seq pipeline to identify causative mutations responsible for a phenotype
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
⛓ Correct misassemblies using linked AND long reads
Create regional association plots from GWAS or meta-analysis
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping