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?

Interactive cell cycle analysis

Mechanistic Pan-Cancer Signaling Model

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

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

"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.

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

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

Molekulaarse rakubioloogia kursuse rakutsükli loeng

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