Repositories list

• PILOT-GM-VAE

  Public
  Patient-Level Analysis of Single Cell Disease Atlas with Optimal Transport of Gaussian Mixtures Variational Autoencoders

  Python

  •

  Other

  •0•0•0•0•Updated Jan 18, 2025Jan 18, 2025

• bulk_RNASeq

  Public
  Bulk RNAseq R pipeline

  R

  •

  Other

  •0•0•0•0•Updated Jan 13, 2025Jan 13, 2025

• pyCrossTalkeR

  Public
  Jupyter Notebook

  •

  MIT License

  •0•1•0•0•Updated Jan 13, 2025Jan 13, 2025

• phlower

  Public
  Use hodge decomposition for trajectory analysis

  single-cellsimplicial-complextrajectory-inference+ 2hodge-laplacianhodge-laplacian-decomposition

  Python

  •

  GNU Affero General Public License v3.0

  •0•4•0•0•Updated Jan 10, 2025Jan 10, 2025

• CrossTalkeR

  Public
  R package to do the Ligand Receptor Analysis Visualization

  networkcell-cell-communicationsingle-cell

  Jupyter Notebook

  •

  MIT License

  •10•41•5•0•Updated Jan 10, 2025Jan 10, 2025

• LR2TF

  Public
  R

  •0•0•0•0•Updated Dec 9, 2024Dec 9, 2024

• PILOT

  Public
  Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)

  single-celldigital-pathologydisease-progression+ 2multi-scale-single-celldisease-trajectory

  Python

  •

  MIT License

  •3•16•1•0•Updated Nov 22, 2024Nov 22, 2024

• reg-gen

  Public
  Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

  bioinformaticsdnase-seqgenomics+ 7ngsmotifchip-seqatac-seqmotif-analysisfootprintingdifferential-peak-calling

  Python

  •

  Other

  •30•106•60•1•Updated Nov 16, 2024Nov 16, 2024

• sigurd

  Public
  Using single cell genotype data, the cells are annotated and analysed.

  R

  •0•6•0•0•Updated Nov 12, 2024Nov 12, 2024

• MOJITOO

  Public
  MOJITOO: a fast and universal method for integration of multimodal single cell data

  R

  •0•10•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

• scrna_seurat_pipeline

  Public
  comprehensive analysis of single-cell transcriptomics data

  R

  •9•19•4•0•Updated Sep 25, 2024Sep 25, 2024

• scMEGA

  Public
  scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference

  grnmultiomicssingle-cell

  R

  •

  Other

  •3•37•9•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

• CimpleG

  Public
  CimpleG, an R package to find (small) CpG signatures.

  rmethylationbiomarker-discovery+ 4deconvolutionbiomarkerscell-type-classificationcpg-signature

  R

  •

  GNU General Public License v3.0

  •0•6•2•0•Updated Dec 13, 2023Dec 13, 2023

• 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•6•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

  •4•25•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

• sc2marker

  Public
  Surface Marker Detection Using Single Cell Data

  marker-detectionsingle-cell

  HTML

  •

  MIT License

  •2•9•2•0•Updated May 6, 2022May 6, 2022

• costalab.github.io

  Public
  The repository for CostaLab website

  HTML

  •

  MIT License

  •0•0•0•0•Updated Apr 27, 2022Apr 27, 2022

• MOJITOO-reproducibility

  Public
  R

  •0•0•0•0•Updated Mar 16, 2022Mar 16, 2022

• RNA_Expression_Analysis_in_Python

  Public
  Jupyter Notebook

  •1•2•0•0•Updated Mar 10, 2022Mar 10, 2022

• cellxgene_submission

  Public
  Code for preparing cellxgene data submission

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Nov 19, 2021Nov 19, 2021

• multi_omics_heart_failure

  Public
  Code for single-cell multiomics analysis of human heart failure

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Nov 11, 2021Nov 11, 2021

• SNPnet

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Aug 3, 2021Aug 3, 2021

• SOSE_2021

  Public
  A repository of materials for the SOSE2021 course of CostaLab

  Shell

  •

  MIT License

  •1•2•0•0•Updated May 17, 2021May 17, 2021