DiagramIt is a browser app for publication-quality lab and experimental-design figures: differentiation timelines, developmental ontogenies (mouse and human embryo, hematopoiesis, C. elegans lineage) that you can prune and edit, well plates, dishes and a library of cell types. Runs in the browser, nothing to install; exports SVG and PNG.

XCell is a browser-based workbench for exploring single cell and spatial transcriptomics data without writing code. You run it locally and open a dataset — h5ad, 10x Genomics h5, a CellRanger matrix folder, Visium HD, or a Seurat object — and get an interactive embedding with pan, zoom, and lasso selection alongside point-and-click pipelines for preprocessing, dimensionality reduction, clustering, differential expression, and trajectory inference, plus tools specific to spatial data. It keeps track of what you did and exports a reproducible Jupyter notebook and a methods paragraph along with the processed data.

IMCell predicts the smallest set of transcription factors you would need to perturb together to convert one cell type into another. It treats the problem as influence maximization over a signed gene regulatory network — the same idea used to find the few people who would best spread information through a social network — and searches for the combination that jointly activates the genes that should go up and represses those that should go down. It returns a TF set rather than a ranked list, and a dynamic mode proposes a sequence of TF sets that moves through intermediate states. Written in R. See also CompForce.

CompForce runs several published methods for predicting the transcription factors that drive a cell identity transition, all on your own data and under one standardized interface. Give it a counts matrix, sample metadata, and a list of transcription factors, name a source and target cell state, and it returns a ranked TF list from each method — differential expression, a CellNet-style network influence score, a Mogrify-style score, and the Jensen-Shannon divergence approach — along with a consensus ranking. It also includes utilities for benchmarking and for simulating whether a predicted TF set would actually produce the intended transition. Written in R, and the companion to IMCell.

DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation