The complete FlowSOM package known from R, now available in Python!

Integrative analysis for scTCR- and scRNA-seq data

Cellsnake tool main repo

Analysis methods for analysing single cell RNA-seq data; particularly with the goal of checking if tentative clusters of cells are significantly different to one another in terms of their gene expr…

🔅 Shapash: User-friendly Explainability and Interpretability to Develop Reliable and Transparent Machine Learning Models

A flexible pipeline for complete analysis of bacterial genomes

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

An interactive heatmap visualization built using D3.js

scRNAseq analysis notes from Ming Tang

Antique or modern atlas-like depictions of non-linear dimensionality reduction for single cell data

A package for the analysis of Imaging Mass Cytometry data

Some tools for plotting single-cell data

R based workflow for multiplexed imaging data

Robust Integration of Single-Cell Cytometry Datasets

Scanpy Tutorials.

Differential expression analysis for single-cell RNA-seq data.

scDIOR: Single cell data IO softwaRe

A tool for semi-automatic cell type classification

A pixel classification based multiplexed image segmentation pipeline

Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR

A game theoretic approach to explain the output of any machine learning model.

Test data to be used for automated testing with the nf-core pipelines

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

Fast visualization tool for large-scale and high dimensional single-cell data

Python Flow Cytometry Calibration Library

A python package for visualization and analysis of high-throughput flow cytometry data