3e78b320f1bd83e1a2fe2dc23fd660d34e186bf6 max Fri Sep 26 09:31:19 2025 -0700 adding examples diff --git README.rst README.rst index 391cb3d..7f04a8a 100644 --- README.rst +++ README.rst @@ -1,30 +1,40 @@ .. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/ucsc-cell-browser/README.html UCSC Single Cell Browser ======================== The UCSC Cell Browser is a viewer for single cell data. You can click on and hover over cells to get meta information, select cells to get annotation histograms, make expression violin plots and heatmaps, search for genes to color on and click clusters to show cluster-specific marker genes. It supports the usual gene expression plots, ATAC, spatial gene/ATAC, multi-modal combinations of these and trajectory lines. It comes with one-line data exporters for all common analysis formats: Seurat, Scanpy, Cellranger, Monocle and you can always use tsv/csv files to import your data. The exporters are part of Seurat 3/4 and Scanpy. -To look at a list of selected single cell datasets, see http://cells.ucsc.edu +Here are a few datasets that demonstrate these features: + +- A simple gene expression dataset: https://cells.ucsc.edu/?ds=cortex-dev +- Spatial transcriptomics support https://ms-subcortical-lesions.cells.ucsc.edu +- Split screen mode to display both the spatial and snRNA-seq data side by side https://cells.ucsc.edu/?ds=dup15q-cortex-organoids+spatial+control +- Cell trajectories from monocle https://cells-test.gi.ucsc.edu/?ds=pre-postnatal-cortex+ex-neu+rna +- Cell trajectories from URD https://cells.ucsc.edu/?ds=cardiac-differentiation+trajectory+cm-combined-trajectory +- Clone lineage tracing support: color by the field CellTag, select tags in the legend, then click "recolor checked": https://cells.ucsc.edu/?ds=gbm-nvp+nvp-celltag +- Brain lipidomics https://cells.ucsc.edu/?ds=brain-lipids + +To show all our > 200 single cell datasets, see http://cells.ucsc.edu To setup your own cell browser, from Cellranger, Seurat, Scanpy or text files (tsv/csv), or just a single cell expression matrix, read the documentation at http://cellbrowser.rtfd.io. If you use the UCSC Cell Browser in your research, please cite `our Bioinformatics paper `_. If you are also using data from a specific dataset we host, please also cite the original authors of that dataset (visible under 'Info & Download' while viewing that dataset). If you want us to add a single cell dataset to the website http://cells.ucsc.edu, please contact us at cells@ucsc.edu. We are happy to add any dataset. This is a viewer for a static, precomputed layout. If you're looking for an interative layout, where you can move the cells around and run some algorithms interactively, try Chan-Zuckerberg's own cellxgene or Spring. A website with both datasets and some analysis is `Scope `_.