rujinlong

rujinlong's Stars

• AppFlowy-IO/AppFlowy

  Bring projects, wikis, and teams together with AI. AppFlowy is an AI collaborative workspace where you achieve more without losing control of your data. The best open source alternative to Notion.

  Language:Dart58.1k3563k3.8k

• logancyang/obsidian-copilot

  THE Copilot in Obsidian

  Language:TypeScript3k29447209

• Ligo-Biosciences/AlphaFold3

  Open source implementation of AlphaFold3

  Language:Python91922680

• adaptyvbio/ProteinFlow

  Versatile computational pipeline for processing protein structure data for deep learning applications.

  Language:Python24281717

• arklumpus/TreeViewer

  Cross-platform software to draw phylogenetic trees

  Language:C#1883479

• LucaOne/LucaOne

  The LucaOne’s code, including model code and pre-training code.

  Language:Python1544821

• steineggerlab/foldmason

  Multiple Protein Structure Alignment at Scale with FoldMason

  Language:C13151013

• shenwei356/LexicMap

  LexicMap: efficient sequence alignment against millions of prokaryotic genomes

  Language:Go110364

• IndexThePlanet/Logan

  Logan Unitigs and Contigs

  1018133

• micom-dev/micom

  Python package to study microbial communities using metabolic modeling.

  Language:Python9454318

• samsledje/D-SCRIPT

  A structure-aware interpretable deep learning model for sequence-based prediction of protein-protein interactions

  Language:Jupyter Notebook8765718

• gbouras13/phold

  Phage Annotation using Protein Structures

  Language:Python854284

• ml4bio/Dense-Homolog-Retrieval

  Nature Biotechnology: Ultra-fast, sensitive detection of protein remote homologs using deep dense retrieval

  Language:Python844212

• COMBINE-lab/cuttlefish

  Building the compacted de Bruijn graph efficiently from references or reads.

  Language:C++837349

• weisberglab/beav

  BEAV: Bacterial Element Annotation reVamped

  Language:Shell58254

• timkartar/DeepPBS

  Geometric deep learning of protein–DNA binding specificity

  Language:Python495146

• jean-pierreBoth/gsearch

  Approximate nearest neighbour search for microbial genomes based on hash metric

  Language:Rust43437

• susiegriggo/Phynteny

  Predict the function of phage hypothetical proteins using an LSTM model trained with Phage Synteny

  Language:PureBasic40553

• TravisWheelerLab/nail

  Nail is an Alignment Inference tooL

  Language:Rust34522

• Matteopaluh/KEMET

  KEGG Module Evaluation Tool

  Language:Python263156

• amillard/tax_myPHAGE

  Workflow to assign Taxonomy to a bacteriophage genome isolate

  Language:Python241172

• Yasas1994/Jaeger

  Jaeger is a quick and precise tool for detecting phages in sequence assemblies.

  Language:Python24741

• d-mcgrath/MetaPathPredict

  A machine learning-based tool for predicting metabolic modules in incomplete bacterial genomes.

  Language:Python16651

• JinsenLi/deepDNAshape

  A method to predict DNA shape features considering farther flanking region.

  Language:Python16542

• robertaboukhalil/alignment-sandbox

  Tool for exploring sequence alignment algorithms

  Language:Svelte13210

• tapj/biotyper

  an R package to biotype a community

  Language:R13339

• jarojasva/HADEG

  Repository of sequences to annotate hydrocarbon-degrading genes/proteins from genomes/metagenomes

  Language:R10221

• samuelmurail/af2_analysis

  Analysis of alphafold and colabfold results

  Language:Jupyter Notebook10323

• Yasas1994/phage_contig_annotator

  Annotates genes on putative phage contigs with protein orthologous groups using PHROGs

  Language:Python5132

• biobakery/waafle

  http://huttenhower.sph.harvard.edu/waafle

  Language:Python4501