Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

• UpdatedOct 23, 2025

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.

• UpdatedJul 7, 2022
• Python

Predict cell cycle phase in a continuum from single-cell RNA-seq data

• UpdatedNov 14, 2020
• R

Track single cells and profile the cell cycle with PCNA fluorescence images

• UpdatedSep 1, 2023
• Python

Single-cell transcriptome analysis by fluorescence labeling

• UpdatedJan 10, 2023
• HTML

• UpdatedOct 8, 2025
• R

Mechanistic Pan-Cancer Signaling Model

• UpdatedFeb 17, 2025
• Jupyter Notebook

What's all this talk about cell cycle models?

• UpdatedOct 17, 2023
• Python

This is to show oscillations in the number of cells in G1 and in G2 phase of cell cycle.

• UpdatedMay 2, 2023
• Jupyter Notebook

Interactive cell cycle analysis

• UpdatedOct 12, 2021
• R

Track single-cells and profile the cell cycle with PCNA images.

• UpdatedJun 9, 2022
• Python

ChIP-exo analysis highlights Fkh1 and Fkh2 transcription factors as hubs that integrate multi-scale networks in budding yeast | T.D.G.A. Mondeel, P. Holland, J. Nielsen and M. Barberis | 2019 |https://doi.org/10.1093/nar/gkz603

• UpdatedMar 8, 2022
• HTML

RB represses cohesin-dependent loop formation and safeguards E2F-independent transcription

• UpdatedSep 29, 2024
• Jupyter Notebook

"Transcriptional Heterogeneity and Cell Cycle Regulation as Central Determinants of Primitive Endoderm Priming" published in eLife (2022)

• UpdatedAug 25, 2022
• MATLAB

Bottom-up dynamical modeling of biological systems using ordinary, partial, and stochastic differential equations.

• UpdatedMay 16, 2024
• MATLAB

Molekulaarse rakubioloogia kursuse rakutsükli loeng

• UpdatedNov 14, 2017

IFAC2020

• UpdatedJul 22, 2025
• MATLAB

Modeling the START transition in the budding yeast cell cycle

• UpdatedAug 4, 2024

An interactive web application for exploring cell cycle models

• UpdatedOct 31, 2023
• Python

Imoto, H. & Okada, M. Signal-dependent regulation of early-response genes and cell cycle: a quantitative view. Curr. Opin. Syst. Biol. 15, 100–108 (2019).

• UpdatedAug 25, 2020
• Julia