Workflow leveraging the scanpy-scripts package to run Scanpy in a Nextflow workflow

Use the Scanpy read 10X dataset and LightGBM run the model

single-cell scanpy teaching

We explore how to use scanpy and besca to analyse single-cell sequencing data

Advanced scanpy environment with R support (rpy2)

Reproducible code for the scRNA-seq analyses in the paper 'The neuroendocrine response to stress at single-cell resolution" by Lopez et al. 2020.

Single cell RNA seq tutorials

Review on Single Cell RNA-sequencing

Analysis of a .loom file containing single-cell RNA-sequencing data. Clustering & UMAP embedding using Scanpy, followed by RNA velocity analysis using scVelo.

Python readers for different data formats for FASTGenomics.

KRAS-mutant pancreatic ductal adenocarcinoma (PDAC) is highly immunosuppressive and resistant to targeted therapies, immune checkpoint blockade and engineered T cells. In this study, we performed a systematic high throughput combinatorial drug screen and identified a synergistic interaction between the MEK inhibitor trametinib and the multi- kin…

Intuitive Nonparametric Gene Network Search Algorithm

IP Scanner (Ping All IP Addresses in the network)

Notes and studies about single-cell RNA-Seq analysis

This repository extends scanpy to handle flow and mass cytometry data.

scRNA-seq data analysis using scanpy

Transcriptomic analysis of the developing mouse habenula

Multimodal datasets, in MuData format