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Metacell - Single-cell mRNA Analysis

R 113 30 Updated Oct 11, 2023

🧠 Visualizing Single Cell and Spatial Transcriptomics

R 47 12 Updated Oct 30, 2024

Accurate and robust imputation of scRNA-seq data

R 95 34 Updated Aug 21, 2019

R package for Pathway RespOnsive GENe activity inference

R 98 19 Updated Jan 30, 2023

This is a short tutorial to show in parallel how to estimate TF and kinase activities from transcriptomic and phosphoproteomic data

R 3 2 Updated Apr 27, 2023

https://www.sc-best-practices.org

Jupyter Notebook 822 198 Updated Jan 18, 2025

code for "An Integrated Clinical, Omic, and Image Atlas of an Evolving Metastatic Breast Cancer"

Python 3 Updated Nov 1, 2021

Analysis of omic and imaging data in pancreatic ductal adenocarcinoma distinguishes liver and lung recurrence and patient outcomes

Jupyter Notebook 5 Updated Nov 13, 2024

Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕

R 173 32 Updated Jun 24, 2021

Code used to analyze snRNAseq data from the developing mouse superior colliculus.

R 1 1 Updated Feb 1, 2023

Generate high quality, publication ready visualizations for single cell transcriptomics data.

R 171 13 Updated Jan 22, 2025

Single cell RNA-seq analysis for transcriptomic type characterization

R 35 3 Updated Jan 17, 2025

Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas

Jupyter Notebook 58 23 Updated Jan 17, 2025

iterative clustering pipeline of big single cell datasets.

R 27 10 Updated Jan 8, 2025

Genearlized mapping scripts for RNA-seq and Patch-seq data

R 11 2 Updated Jan 15, 2025

This github repository contains the data files and analysis code used in "Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell …

R 4 2 Updated Feb 6, 2023

reticulate-free single cell format conversion

R 111 6 Updated Dec 6, 2024

LIANA: a LIgand-receptor ANalysis frAmework

R 188 31 Updated Aug 7, 2024
Jupyter Notebook 1 Updated Jul 1, 2024

A computational method scSemiProfiler that provides affordable single-cell data for large-scale disease cohorts using deep generative model.

Jupyter Notebook 20 2 Updated Dec 26, 2024

R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data

R 26 9 Updated Jun 8, 2024

general repo that holds all analysis and figures for the thymus spatial atlas by Yayon, Kedlian, Boehme, Radtke and many more!

Jupyter Notebook 10 2 Updated Nov 20, 2024

Python package to interactively annotate histological images within a jupyter notebook

Jupyter Notebook 13 4 Updated Nov 6, 2024

Collections of library structure and sequence of popular single cell genomic methods

HTML 446 95 Updated Dec 10, 2024

Analysis notebooks for G2G MS

Jupyter Notebook 6 Updated Oct 7, 2024

Aligning gene expression trajectories of single-cell reference and query systems

Jupyter Notebook 52 5 Updated Oct 14, 2024

Inference of TCR motifs

Jupyter Notebook 28 3 Updated Jan 17, 2025

Contains code to analyse the data from the paper: Immune profiling-based targeting of pathogenic T cells with ustekinumab in ANCA-associated glomerulonephritis

Jupyter Notebook 4 1 Updated Sep 21, 2024
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