All

47 repositories

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•1•1•Updated Apr 22, 2026Apr 22, 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
•
Other
•2•8•0•0•Updated Apr 22, 2026Apr 22, 2026
pyCrossTalkeR
Public
pyCrossTalkeR is a framework for network analysis and visualisation of Ligand Receptor networks
Jupyter Notebook
•
MIT License
•1•3•0•2•Updated Apr 22, 2026Apr 22, 2026
sc2marker
Public
Surface Marker Detection Using Single Cell Data
single-cell marker-detection
single-cell marker-detection
HTML
•
MIT License
•3•12•2•0•Updated Apr 21, 2026Apr 21, 2026
scrna_seurat_pipeline
Public
comprehensive analysis of single-cell transcriptomics data
R
•9•25•4•0•Updated Apr 8, 2026Apr 8, 2026
CostaLab_python_integration
Public
0•0•0•0•Updated Apr 7, 2026Apr 7, 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
•9•49•3•0•Updated Mar 24, 2026Mar 24, 2026
NicheSphere
Public
Python
•
MIT License
•1•3•2•0•Updated Mar 20, 2026Mar 20, 2026
scACCorDiON.su
Public
R
•
Other
•0•0•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
LR2TF
Public
R
•0•1•0•0•Updated Nov 13, 2025Nov 13, 2025
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
•
GNU Affero General Public License v3.0
•2•24•5•0•Updated Nov 12, 2025Nov 12, 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
•
Other
•29•114•66•2•Updated Nov 3, 2025Nov 3, 2025
Resources
Public
Resources our lab likes :)
0•1•0•0•Updated Oct 7, 2025Oct 7, 2025
scACCorDiON
Public
Comparing Directed Weighted Graphs
Jupyter Notebook
•
MIT License
•1•4•0•0•Updated Sep 19, 2025Sep 19, 2025
sigurd
Public
R
•0•1•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•11•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•45•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
scopen
Public
scOpen: single-cell open chromatin analysis via NMF modelling
Python
•
GNU General Public License v3.0
•3•28•2•0•Updated Feb 4, 2023Feb 4, 2023
CostaLab_PhD_Thesis_Template
Public
This is a Latex template for PhD thesis in Costalab
TeX
•
MIT License
•0•0•0•0•Updated Aug 26, 2022Aug 26, 2022
mouse_heart_MI
Public
Codes for analysis of mouse heart MI scATAC-seq data
R
•
MIT License
•0•0•0•0•Updated Jun 7, 2022Jun 7, 2022
spatial_multiomic_mi
Public
HTML
•0•0•0•0•Updated May 13, 2022May 13, 2022
SOSE2022
Public
Material for the spring course sc(RNA+ATAC)
MIT License
•0•0•0•0•Updated May 6, 2022May 6, 2022

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CostaLab

All

All

47 repositories

PILOT

PILOT-GM-VAE

pyCrossTalkeR

sc2marker

scrna_seurat_pipeline

CostaLab_python_integration

CrossTalkeR

NicheSphere

scACCorDiON.su

example_clust_bm_plots

CimpleG

LR2TF

phlower

reg-gen

Resources

scACCorDiON

sigurd

VT3-ISMB-ECCB

bulk_RNASeq

MOJITOO

phlower-reproducibility

scMEGA

kidney_injury_lineage

ArchRNA

scopen-reproducibility

scopen

CostaLab_PhD_Thesis_Template

mouse_heart_MI

spatial_multiomic_mi

SOSE2022

All

All

Repositories list

47 repositories