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

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.

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

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

Single-cell transcriptome analysis by fluorescence labeling

What's all this talk about cell cycle models?

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

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

Mechanistic Pan-Cancer Signaling Model

Interactive cell cycle analysis

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

Molekulaarse rakubioloogia kursuse rakutsükli loeng

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

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

Modeling the START transition in the budding yeast cell cycle

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).

PyTorch + images of human T lymphocyte cells (Jurkat cells)

Deep Learning algorithm to predict the cell cycle phase using circular regression

Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs | Thierry D.G.A. Mondeel, Oleksandr Ivanov, Hans V. Westerhoff, Wolfram Liebermeister and Matteo Barberis | NPJ Syst. Biol. Appl. (2020) | https://doi.org/10.1038/s41540-020-0125-0