Single Cell Rna Seq

totalVIPython

A Python library for deep probabilistic modeling and analysis of single-cell and spatial omics data.

RNA-seq AnalysisPython

A comprehensive collection of notes, tutorials, and resources for RNA-seq data analysis, covering alignment, quantification, differential expression, and more.

HarmonyR

Fast, sensitive, and accurate integration of single-cell RNA-seq data across multiple datasets, batches, or experimental conditions.

SquidpyPython

A scalable Python toolkit for analyzing and visualizing spatial molecular data from tissue sections.

DoubletFinderR

An R package that predicts doublets (multiple cells mistaken as one) in single-cell RNA sequencing data using artificial nearest neighbor analysis.

scVeloPython

A scalable Python toolkit for RNA velocity analysis in single cells using dynamical modeling.

SCENICHTML

An R package to infer gene regulatory networks and identify cell types from single-cell RNA-seq data.

CellTypistPython

An automated cell type annotation tool for single-cell RNA-seq data using logistic regression classifiers.

GEARSPython

A geometric deep learning model that predicts transcriptional outcomes of single and multi-gene perturbations from single-cell RNA-seq data.

scBERTPython

A BERT-based foundation model pretrained on large-scale scRNA-seq data for automated cell type annotation in single-cell analysis.