Repository Index

Open source code for AlphaFold 2.

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

• pytorch
• protein-structure
• alphafold2

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

• drug-repurposing
• deep-learning
• drug-target-interactions
• toolkit

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

• spark
• big-data
• bioinformatics
• genomics

:christmas_tree:Visualization and annotation of phylogenetic trees

• r
• visualization
• phylogenetic-trees
• annotations

[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome

• dataset
• dna
• dna-processing
• dna-training

The repository host gives no description.

Multi-Omics Factor Analysis

• multi-omics
• factor-analysis
• mofa

Native R and Python sample-deletion robustness for omics: candidate certificates, minimum deletion bounds, Bioconductor model refits and donor-level pseudobulk

• bioinformatics
• exact-optimization
• metabolomics
• paired-data

MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction (Bioinformatics)

LLM for Drug Editing, ICLR 2024

• chatgpt
• conversation
• drug
• drug-discovery

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

• disentanglement
• drug-discovery
• genomics
• perturbation

TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524

• self-attention
• compound-protein-interaction
• transformercpi
• structure-free-virtual-sreening

Data visualisation web components for the life sciences.

• biohackeu21
• bioinformatics
• visualization
• webcomponents

PyTorch implementation of the MIDAS algorithm for single-cell multimodal data integration (Nature Biotechnology 2024).

• deep-generative-model
• deep-learning
• single-cell-data-integration
• single-cell-multiomics

The framework for quantification of neuronal anatomy

• neuroscience
• neuroanatomy-toolbox
• imagej
• imagej2

High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations

Predicting Cell Health with Morphological Profiles

• carpenter-lab
• morphological-profiling
• crispr
• cell-painting

gateway for segmentation data to Rstats & visualization with ggplot2 - in development

• visualization
• fluorescence-data
• ggplot

Interpretable drug response prediction with graph neural networks over drugs, cell lines, and genes.