Single-cell analysis in Python. Scales to >1M cells.

Annotated data.

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

muon is a multimodal omics Python framework

Cell type annotation with local Large Language Models (LLMs) - Ensuring privacy and speed with extensive customized reports

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.

Convert between AnnData and SingleCellExperiment

Learning cell communication from spatial graphs of cells

Bring your single-cell data to life

pseudobulking on an AnnData object

Translates an AnnData object with mouse gene symbols into one with human gene symbols by mapping orthologs from biomart.

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

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

An easy-to-use PyTorch implementation of Automatic Cell-Types Identification of single-cell RNA sequencing using Neural Networks (ACTINN)

MiCV is a python dash-based web-application that enables researchers to upload raw scRNA-seq data and perform filtering, analysis, and manual annotation.

orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.

Notes and studies about single-cell RNA-Seq analysis

Sobolev alignment of deep probabilistic models for comparing single cell profiles

single-cell scanpy teaching

Review on Single Cell RNA-sequencing