Repository Index

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

• fastq
• qc
• preprocessing
• filtering

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

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

A Go package for engineering organisms.

• synthetic-biology
• synbio
• genetic-engineering
• molecular-biology

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

A Network Integration Approach for Drug-Target Interaction Prediction

Open-source software for exploring and analyzing large, high-dimensional image-derived data.

• cellprofiler-analyst
• cellprofiler
• image-analysis
• machine-learning

🏃 The go-to single-cell Foundation Model

• batch-correction
• cell-biology
• celltype-annotation
• denoising

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

Interpretable bilinear attention network with domain adaptation improves drug-target prediction.

BulkFormer: A large-scale foundation model for human bulk transcriptomes

NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions

• computational-biology
• bioinformatics
• graph-convolution
• deep-learning

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