Ron Finn's repositories
rapids_singlecell
Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.
admet_ai
Training and prediction scripts for Chemprop models trained on ADMET datasets
ArchRtoSignac
An R package performing object conversion from ArchRProject (ArchR) to Signac SeuratObject (Signac)
awesome-AI4MolConformation-MD
List of molecules (small molecules, RNA, peptide, protein, enzymes, antibody, and PPIs) conformations and molecular dynamics (force fields) using generative artificial intelligence and deep learning
awesome_neuropixels
A curated list of awesome Neuropixels resources.
Cascade
Calibrated inference of spiking from calcium ΔF/F data using deep networks
cdk
The Chemistry Development Kit
cell2cell
User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
cellxgene
An interactive explorer for single-cell transcriptomics data
chromVAR
chromatin Variability Across Regions (of the genome!)
ClusterGVis
One-step to Cluster and Visualize Gene Expression Matrix
deepchem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
demuxalot
Reliable, scalable, efficient demultiplexing for single-cell RNA sequencing
DrugHIVE
DrugHIVE: Structure-based drug design with a deep hierarchical generative model
escape
Easy single cell analysis platform for enrichment
EvoBind
In silico directed evolution of peptide binders with AlphaFold
ggsc
🧠 Visualizing Single Cell and Spatial Transcriptomics
GseaVis
An implement R package to visualize GSEA results
HuMMuS
Molecular interactions inference from single-cell multi-omics data
irGSEA
The integration of single cell rank-based gene set enrichment analysis
jsoncrack.com
✨ Innovative and open-source visualization application that transforms various data formats, such as JSON, YAML, XML, CSV and more, into interactive graphs.
KAZU
Fast, world class biomedical NER
LLMs-from-scratch
Implementing a ChatGPT-like LLM in PyTorch from scratch, step by step
PyComplexHeatmap
PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)
scELMo
Codes for paper: scELMo: Embeddings from Language Models are Good Learners for Single-cell Data Analysis
scHGR
An automated cell identity annotation tool, termed single-cell Hybrid graph neural network with Gene Regulations (scHGR)
torchdrug
A powerful and flexible machine learning platform for drug discovery
voyager
From geospatial to spatial -omics