QuaDBio Lab

All

34 repositories

cellmapper
Public
k-NN-based mapping of cells across representations to transfer labels, embeddings, and expression values.
genomics scrna-seq data-integration representation-learning single-cell k-nn spatial-biology
Python
•
MIT License
•0•2•3•1•Updated May 5, 2025May 5, 2025
slurm_sweep
Public
Hyperparameter sweeps on SLURM clusters
Python
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MIT License
•0•1•1•1•Updated May 5, 2025May 5, 2025
ecosystem-packages
Public
Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
Python
•
BSD 3-Clause "New" or "Revised" License
•49•0•0•0•Updated May 2, 2025May 2, 2025
morphodynamics_human_brain_organoid
Public
Jupyter Notebook
•1•1•0•0•Updated Apr 17, 2025Apr 17, 2025
iNeuron_morphogens
Public
Jupyter Notebook
•0•0•0•0•Updated Apr 17, 2025Apr 17, 2025
cell-annotator
Public
Automatically annotate cell types, consistently across samples.
annotation genomics scrna-seq single-cell llm
Python
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MIT License
•1•11•5•1•Updated Apr 17, 2025Apr 17, 2025
BVO_fate_and_state_transitions
Public
R
•
GNU General Public License v3.0
•0•4•0•0•Updated Apr 11, 2025Apr 11, 2025
scib-metrics
Public
Accelerated, Python-only, single-cell integration benchmarking metrics
Python
•
BSD 3-Clause "New" or "Revised" License
•16•0•0•0•Updated Apr 10, 2025Apr 10, 2025
simple_slurm
Public
A simple Python wrapper for Slurm with flexibility in mind.
Python
•
GNU Affero General Public License v3.0
•23•0•0•0•Updated Apr 8, 2025Apr 8, 2025
HNOCA-tools
Public
Toolbox of the Human Neural Organoid Cell Atlas
Jupyter Notebook
•
GNU General Public License v3.0
•1•0•0•0•Updated Apr 1, 2025Apr 1, 2025
scRNAseq_analysis_vignette
Public
Tutorial for scRNA-seq data analysis beginners using R
bioinformatics tutorial single-cell-rna-seq single-cell-analysis
66•195•2•0•Updated Mar 5, 2025Mar 5, 2025
scRNAseq_analysis_python_vignette
Public
Tutorial of scRNA-seq data analysis with Python
HTML
•0•3•0•0•Updated Mar 5, 2025Mar 5, 2025
sopa
Public
Technology-invariant pipeline for spatial omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells
Python
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BSD 3-Clause "New" or "Revised" License
•31•0•0•0•Updated Feb 21, 2025Feb 21, 2025
spatialdata-plot
Public
Static plotting for spatialdata
Python
•
BSD 3-Clause "New" or "Revised" License
•16•0•0•0•Updated Feb 21, 2025Feb 21, 2025
amex_merfish_spaceolotl
Public
Python
•0•0•0•0•Updated Jan 6, 2025Jan 6, 2025
analysis_template
Public template
Simple template repo for single-cell/spatial analysis
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Nov 10, 2024Nov 10, 2024
RNAseq_tutorial
Public
8•27•0•0•Updated Oct 16, 2024Oct 16, 2024
moscot
Public
Multi-omic single-cell optimal transport tools
Python
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BSD 3-Clause "New" or "Revised" License
•10•0•0•0•Updated Jul 26, 2024Jul 26, 2024
Tangram
Public
Spatial alignment of single cell transcriptomic data.
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•56•0•0•0•Updated Jul 3, 2024Jul 3, 2024
scMultiome_analysis_vignette
Public
Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis
tutorial single-cell-rna-seq single-cell-analysis single-cell-atac-seq single-cell-multiomics bioinformatics
14•56•6•0•Updated Apr 22, 2024Apr 22, 2024
Pando
Public
Multiome GRN inference.
transcriptomics single-cell epigenomics
R
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MIT License
•22•121•21•3•Updated Apr 19, 2024Apr 19, 2024
organoid_epigenomics
Public
R
•1•7•1•0•Updated Apr 12, 2024Apr 12, 2024
simspec
Public
Calculation of Reference/Cluster Similarity Spectrum (RSS/CSS)
batch-correction single-cell-analysis
R
•3•31•5•0•Updated Mar 6, 2024Mar 6, 2024
VoxHunt
Public
VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps
single-cell organoids
HTML
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MIT License
•6•46•2•0•Updated Mar 1, 2024Mar 1, 2024
latent-lego
Public
Latent spaces for single cells
Jupyter Notebook
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MIT License
•0•21•0•0•Updated Oct 31, 2023Oct 31, 2023
iTracer_analysis
Public
Scripts to analyze iTracer data
HTML
•1•9•0•0•Updated Oct 20, 2023Oct 20, 2023
itraceR
Public
The R package to preprocess barcode and scar data of iTracer
R
•0•0•0•0•Updated Oct 16, 2023Oct 16, 2023
organoid_regulomes
Public
Reproducibility code for the manuscript: 'Inferring and perturbing cell fate regulomes in human cerebral organoids
R
•8•28•4•0•Updated Aug 8, 2023Aug 8, 2023
spatial_multimodal_retinal_organoid
Public
R
•1•10•1•0•Updated Apr 7, 2023Apr 7, 2023
scRNAseq_comparison_vignette
Public
Tutorial of condition comparison analysis of scRNA-seq data
bioinformatics tutorial single-cell-rna-seq single-cell-analysis
0•9•0•0•Updated Jul 18, 2022Jul 18, 2022