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?

Mechanistic Pan-Cancer Signaling Model

Interactive cell cycle analysis

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

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

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

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

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

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

Molekulaarse rakubioloogia kursuse rakutsükli loeng

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

Modeling the START transition in the budding yeast cell cycle

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

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