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Added scClustViz
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innesbre authored and seandavi committed May 13, 2019
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Expand Up @@ -256,6 +256,7 @@ List of software packages (and the people developing these methods) for single-c
- [iSEE](https://bioconductor.org/packages/iSEE/) - [R] - iSEE, interactive SummarizedExperiment Explorer. The iSEE package aims to provide an interactive user interface for exploring data in objects derived from the SummarizedExperiment class. Particular focus will be given to single-cell data in the SingleCellExperiment derived class. The interface is implemented with RStudio's Shiny, with a multi-panel setup for ease of navigation. Features include: dynamically linked charts, support for reproducibility by recording the exact code for every output, as well as guided tours to learn step-by-step the salient features of the user interface and of the data. A demo instance of the app is available at this address: http://shiny.imbei.uni-mainz.de:3838/iSEE.
- [NASQAR](http://nasqar.abudhabi.nyu.edu/) - Nucleic Acid SeQuence Analysis Resource, a web-based platform that provides an intuitive interface for popular tools (like DESeq2, Seurat, and others) to perform standard downstream analysis workflows for RNAseq data. The portal hosts a number of R Shiny apps.
- [PIVOT](https://github.com/qinzhu/PIVOT) - Platform for Interactive analysis and Visualization Of Transcriptomics data. [ref](https://doi.org/10.1186/s12859-017-1994-0)
- [scClustViz](https://baderlab.github.io/scClustViz/) - An interactive R Shiny tool for visualizing single-cell RNAseq clustering results from common analysis pipelines (SingleCellExperiment or Seurat, currently). Its main goal is two-fold: A: to help select a biologically appropriate resolution or K from clustering results by assessing differential expression between the resulting clusters; and B: help annotate cell types and identify marker genes. [See the demo app here!](https://innesbt.shinyapps.io/scclustvizdemoapp/) scClustViz can also be used to generate R data packages for sharing published data - see the website for details and a list of published datasets.
- [SeuratWizard](https://github.com/nasqar/SeuratWizard/) - a web-based (wizard style) interactive R Shiny application to perform guided single-cell RNA-seq data analysis and clustering. [demo](http://nasqar.abudhabi.nyu.edu/SeuratWizard)
- [SeuratV3Wizard](https://github.com/nasqar/seuratv3wizard) - a web-based (wizard style) interactive R Shiny application to perform guided single-cell RNA-seq data analysis and clustering based on Seurat v3. [demo](http://nasqar.abudhabi.nyu.edu/SeuratV3Wizard/)
- [ShinyCortex](https://bioinf.eva.mpg.de/shiny/sample-apps/ShinyCortex/) - a resource that brings together data from recent scRNA-seq studies of the developing cortex for further analysis. ShinyCortex is based in R and displays recently published scRNA-seq data from the human and mouse cortex in a comprehensible, dynamic and accessible way, suitable for data exploration by biologists. [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5962798/)
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