CostaLab repositories

52 repositories

pyCrossTalkeR
Public
pyCrossTalkeR is a framework for network analysis and visualisation of Ligand Receptor networks
Jupyter Notebook
•
MIT License
•1•3•4•0•Updated Sep 21, 2026Sep 21, 2026
spatial_sigurd_py
Public
Python implementation of SIGURD with spatial clone detection.
Python
•
MIT License
•0•0•0•0•Updated Sep 21, 2026Sep 21, 2026
AtlasOT
Public
AtlasOT - The Fused Unbalanced Gromov-Wasserstein for Multimodal Integration of Disease Atlases
Jupyter Notebook
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MIT License
•0•1•1•0•Updated Sep 15, 2026Sep 15, 2026
NicheSphere
Public
Python
•
MIT License
•1•5•0•0•Updated Sep 10, 2026Sep 10, 2026
NicheSphere_paper_analysis
Public
This repository contains the necessary code to reproduce the bioinformatic analysis done for the NicheSphere paper on PIC-seq, myelofibrosis (MF) scRNA, and COD…
Jupyter Notebook
•0•0•0•0•Updated Sep 10, 2026Sep 10, 2026
CODEX_pipeline
Public
This repository contains a working example of CODEX data analysis.
Jupyter Notebook
•0•0•0•0•Updated Sep 9, 2026Sep 9, 2026
IntraTalker
Public
R
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Other
•0•2•0•0•Updated Aug 31, 2026Aug 31, 2026
IntraTalkerpy
Public
Performing Intracellular analysis and Gene Expression Perturbations
scrna-seq-analysis cell-cell-communication intracellular-regulations
scrna-seq-analysis cell-cell-communication intracellular-regulations
Python
•
MIT License
•0•1•0•0•Updated Aug 30, 2026Aug 30, 2026
PILOT
Public
Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)
single-cell digital-pathology disease-progression
single-cell digital-pathology disease-progression multi-scale-single-cell disease-trajectory
Python
•
MIT License
•8•26•0•1•Updated Aug 27, 2026Aug 27, 2026
scACCorDiON
Public
Comparing Directed Weighted Graphs
Jupyter Notebook
•
MIT License
•1•6•0•0•Updated Aug 21, 2026Aug 21, 2026
CostaLab_python_integration
Public
Python
•1•0•1•0•Updated Aug 20, 2026Aug 20, 2026
CrossTalkeR
Public
R package to do the Ligand Receptor Analysis Visualization
network single-cell cell-cell-communication
network single-cell cell-cell-communication
Jupyter Notebook
•
MIT License
•10•50•3•0•Updated Aug 18, 2026Aug 18, 2026
scrna_seurat_pipeline
Public
comprehensive analysis of single-cell transcriptomics data
R
•8•25•4•0•Updated Jul 14, 2026Jul 14, 2026
PILOT-GM-VAE
Public
Patient-Level Analysis of Single Cell Disease Atlas with Optimal Transport of Gaussian Mixtures Variational Autoencoders
single-cell optimal-transport variational-autoencoder
single-cell optimal-transport variational-autoencoder disease-progression guassian-mixture-model multi-scale-single-cell
Python
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Other
•3•10•1•0•Updated May 28, 2026May 28, 2026
phlower
Public
Use hodge decomposition for trajectory analysis
single-cell simplicial-complex trajectory-inference
single-cell simplicial-complex trajectory-inference hodge-laplacian hodge-laplacian-decomposition
Python
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GNU Affero General Public License v3.0
•2•26•5•0•Updated May 11, 2026May 11, 2026
sc2marker
Public
Surface Marker Detection Using Single Cell Data
single-cell marker-detection
single-cell marker-detection
HTML
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MIT License
•5•13•2•0•Updated Apr 21, 2026Apr 21, 2026
scACCorDiON.su
Public
R
•
Other
•0•2•0•0•Updated Dec 17, 2025Dec 17, 2025
example_clust_bm_plots
Public
R
•1•0•0•0•Updated Dec 16, 2025Dec 16, 2025
CimpleG
Public
CimpleG, an R package to find (small) CpG signatures.
r methylation biomarker-discovery
r methylation biomarker-discovery deconvolution biomarkers cell-type-classification cpg-signature
R
•
GNU General Public License v3.0
•0•8•0•0•Updated Dec 5, 2025Dec 5, 2025
reg-gen
Public
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
bioinformatics dnase-seq genomics
bioinformatics dnase-seq genomics ngs motif chip-seq atac-seq motif-analysis footprinting differential-peak-calling
Python
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Other
•29•113•66•2•Updated Nov 3, 2025Nov 3, 2025
Resources
Public
Resources our lab likes :)
0•1•0•0•Updated Oct 7, 2025Oct 7, 2025
sigurd
Public
R
•0•2•0•0•Updated Aug 12, 2025Aug 12, 2025
VT3-ISMB-ECCB
Public
HTML
•0•0•0•0•Updated Jul 17, 2025Jul 17, 2025
bulk_RNASeq
Public
Bulk RNAseq R pipeline
R
•
Other
•0•0•0•0•Updated Jan 13, 2025Jan 13, 2025
MOJITOO
Public
MOJITOO: a fast and universal method for integration of multimodal single cell data
R
•1•13•0•0•Updated Oct 23, 2024Oct 23, 2024
phlower-reproducibility
Public
Source code for the reproducibility of the PHLOWER manuscript
R
•0•1•0•0•Updated Oct 15, 2024Oct 15, 2024
scMEGA
Public
scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference
single-cell grn multiomics
single-cell grn multiomics
R
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Other
•3•46•12•0•Updated Sep 20, 2024Sep 20, 2024
kidney_injury_lineage
Public
Lineage tracing reveals transient phenotypic adaptation of tubular cells during acute kidney injury
R
•0•0•0•0•Updated Feb 10, 2024Feb 10, 2024
ArchRNA
Public
ArchR extension to analyze single cells transcriptome
Jupyter Notebook
•0•0•0•0•Updated Feb 28, 2023Feb 28, 2023
scopen-reproducibility
Public
A repository to include all scripts and codes for reproducibility of scOpen manuscript
HTML
•1•7•1•0•Updated Feb 16, 2023Feb 16, 2023

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CostaLab

All

52 repositories

pyCrossTalkeR

spatial_sigurd_py

AtlasOT

NicheSphere

NicheSphere_paper_analysis

CODEX_pipeline

IntraTalker

IntraTalkerpy

PILOT

scACCorDiON

CostaLab_python_integration

CrossTalkeR

scrna_seurat_pipeline

PILOT-GM-VAE

phlower

sc2marker

scACCorDiON.su

example_clust_bm_plots

CimpleG

reg-gen

Resources

sigurd

VT3-ISMB-ECCB

bulk_RNASeq

MOJITOO

phlower-reproducibility

scMEGA

kidney_injury_lineage

ArchRNA

scopen-reproducibility

Repositories list

52 repositories