gomez-dan

Genomics, Big Data-Omics, Multiorgan Bioscientist, Molecular Biologist and Bioinformatician. Master's Student @ Cal State East Bay & Stanford Medicine

@StanfordBioinformatics @MoTrPACSF Bay Area

Pinned Repositories

codex-pipeline
CODEX data processing code
Language:Python1 0 00
cwltool
Common Workflow Language reference implementation
Language:Python10
danieljgomez
Professional Page
Language:SCSS1 1 00
gomez-dan
1 1 00
hra-notebooks
Fun and Interesting Python Notebooks that use the HRA
Language:Jupyter Notebook00
molformer
Repository for MolFormer
Language:Jupyter Notebook10
monkeybread
Analyzing cellular niches in spatial transcriptomics data
Language:Python00
protein_bert
Language:Jupyter Notebook10
SPACEc
Language:Jupyter Notebook00
spatialecotyper
Spatial EcoTyper is a machine learning framework for systematic identification of spatially distinct multicellular communities from single-cell spatial transcriptomics data.
Language:R00

gomez-dan's Repositories

gomez-dan/codex-pipeline
CODEX data processing code
Language:Python1 0 00
gomez-dan/cwltool
Common Workflow Language reference implementation
Language:Python10
gomez-dan/danieljgomez
Professional Page
Language:SCSS1 1 00
gomez-dan/gomez-dan
1 1 00
gomez-dan/gomez-dan.github.io
Daniel's webpage
Language:HTML1 1 00
gomez-dan/gtex-v8
Notebooks and scripts for reproducing analyses and figures from the V8 GTEx Consortium paper
Language:Jupyter Notebook1 0 00
gomez-dan/liana-py
LIANA+: an all-in-one framework for cell-cell communication
Language:Python1 0 00
gomez-dan/maxfuse
Language:Jupyter Notebook1 0 00
gomez-dan/molformer
Repository for MolFormer
Language:Jupyter Notebook10
gomez-dan/protein_bert
Language:Jupyter Notebook10
gomez-dan/sma
Language:Jupyter Notebook1 0 0
gomez-dan/SpaMTP
User Friendly Spatial Metabolomic Data Analysis Package
Language:R1
gomez-dan/stellar
Language:Jupyter Notebook1 0 00
gomez-dan/vitessceR
R API and htmlwidget for Vitessce
Language:R1 0 00
gomez-dan/hra-notebooks
Fun and Interesting Python Notebooks that use the HRA
Language:Jupyter Notebook00
gomez-dan/intro_dgm
"Deep Generative Modeling": Introductory Examples
Language:Jupyter Notebook0 0 00
gomez-dan/monkeybread
Analyzing cellular niches in spatial transcriptomics data
Language:Python00
gomez-dan/SPACEc
Language:Jupyter Notebook00
gomez-dan/spatialecotyper
Spatial EcoTyper is a machine learning framework for systematic identification of spatially distinct multicellular communities from single-cell spatial transcriptomics data.
Language:R00
gomez-dan/CHM13
The complete sequence of a human genome
0 0
gomez-dan/DNABERT_2
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
gomez-dan/ExerkineNet
ExerkineNet is a computational method to generate exerkines from bulk RNA-seq, ATAC-seq, Global Proteomics, Metabolites & Lipidomics, and Immunoassays
Language:Python
gomez-dan/gtex-pipeline
GTEx & TOPMed data production and analysis pipelines
Language:Python0 0
gomez-dan/nichenetr
NicheNet: predict active ligand-target links between interacting cells
gomez-dan/NuFold
NuFold: End-to-End Approach for RNA Tertiary Structure Prediction with Flexible Nucleobase Center Representation
Language:Jupyter Notebook
gomez-dan/ott
Optimal transport tools implemented with the JAX framework, to get differentiable, parallel and jit-able computations.
Language:Python0 0
gomez-dan/RNAPath
Self-supervised representation learning combining GTEx histology, RNA-seq and WGS
gomez-dan/scGPT
scGPT fine-tuned with CELLama
Language:Jupyter Notebook0 0
gomez-dan/scirpy
A scanpy extension to analyse single-cell TCR and BCR data.
Language:Python
gomez-dan/TOSICA
Transformer for One-Stop Interpretable Cell-type Annotation