Scripts for using scanpy
☆39Oct 20, 2025Updated 5 months ago
Alternatives and similar repositories for scanpy-scripts
Users that are interested in scanpy-scripts are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Scripts to install as a Bioconda package for making workflows☆18Sep 15, 2024Updated last year
- Analysis notebooks for "SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes".☆14Nov 20, 2020Updated 5 years ago
- Unbiased single-cell transcriptomic data cell type identification☆15May 7, 2024Updated last year
- Single cell RNA Seq data analysis with quantitative phenotypes☆13Nov 17, 2020Updated 5 years ago
- Consistent Clusters for scRNA-seq☆11Oct 6, 2021Updated 4 years ago
- Calculation of Reference/Cluster Similarity Spectrum (RSS/CSS)☆40Mar 6, 2024Updated 2 years ago
- Code for the empty droplet and cell detection project from the HCA Hackathon.☆21Feb 26, 2019Updated 7 years ago
- Hera-T, a fast and accurate tool for estimating gene abundances in single cell data generated by the 10X-Chromium protocol☆18Nov 9, 2021Updated 4 years ago
- Here I show how to use Deep Autoencoders for single cell RNA sequencing data analysis☆19May 5, 2019Updated 6 years ago
- Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments☆10Mar 13, 2021Updated 5 years ago
- A quick recap of widely used differential analyses methods in R for RNA-seq experiments☆16Dec 7, 2024Updated last year
- SIB/Scilifelab autumn school in single cell omics 2019.☆22Oct 28, 2019Updated 6 years ago
- Analysis of snRNA-seq2 data coming from 3 months old mouse liver, dissecting the influence ploidy has on gene expression.☆14Dec 6, 2021Updated 4 years ago
- Python package to perform normalization and variance-stabilization of single-cell data☆27Jul 17, 2025Updated 8 months ago
- Hierarchical Random Forest for Information Transfer☆13May 26, 2021Updated 4 years ago
- Scanpy Tutorials.☆235Updated this week
- Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support☆41Jan 31, 2024Updated 2 years ago
- Sanger Cellular Genetics single-cell ATAC-seq pipeline.☆13Aug 25, 2023Updated 2 years ago
- Scripts used to perform analyses in Rice et al. (2023)☆16Dec 28, 2023Updated 2 years ago
- Human pan-genome analysis pipeline☆31Apr 30, 2020Updated 5 years ago
- Transcriptional regulatory network inference from gene expression and prior information with LASSO-StARS☆15May 3, 2022Updated 3 years ago
- Single Cell Epigenome-based Inference of Activity☆19Sep 27, 2023Updated 2 years ago
- ☆12Jan 31, 2023Updated 3 years ago
- Scripts and notebooks used in Akgol Oksuz et al. paper☆11Jan 18, 2021Updated 5 years ago
- Notes on SNP-related tools and genome variation analysis☆28Aug 30, 2025Updated 6 months ago
- cluster stability measurement by subsampling and reclustering with Seurat V3 and V4☆11Jul 9, 2021Updated 4 years ago
- A wrapper around the sleepwalk package that allows for interactive knn visualizations of an embedding.☆22May 8, 2024Updated last year
- ATAC-seq processing pipeline☆34Apr 8, 2022Updated 3 years ago
- ☆16May 13, 2022Updated 3 years ago
- Shiny app for visualization, exploration of mouse brain single cell gene expression☆11Oct 31, 2018Updated 7 years ago
- Constructing gene regulatory networks by integrating scRNA-seq and scATAC-seq data☆13Dec 7, 2021Updated 4 years ago
- Automated cell filtering for single-cell RNA sequencing data☆26Nov 14, 2023Updated 2 years ago
- A machine-learning algorithm to predict CTCF-mediated long-range chromatin interactions☆17Nov 7, 2018Updated 7 years ago
- Transposable element expression at unique loci in single cells with CELLO-seq☆11Jun 17, 2024Updated last year
- 🍹This repo includes the scripts and analysis notebook for the Droplet Hi-C manuscript☆15Feb 6, 2026Updated last month
- Repository for all R scripts used for the bioinformatic analyses of the mouse and human 10x Genomics Visium spatially resolved transcript…☆31Jul 13, 2024Updated last year
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆80Jan 24, 2025Updated last year
- ☆12Jul 6, 2023Updated 2 years ago
- A mosaic genome painting tool for plant genomes☆18Mar 4, 2025Updated last year