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Update README.md
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seandavi authored Jul 8, 2024
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Expand Up @@ -492,6 +492,7 @@ imputing missing gene expression measurements](https://arxiv.org/pdf/1905.02269.
- [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.
- [scRNAseqApp](https://bioconductor.org/packages/scRNAseqApp/) - The scRNAseqApp is a Shiny app package designed for interactive visualization of single-cell data. It is an enhanced version derived from the [ShinyCell](https://github.com/SGDDNB/ShinyCell), repackaged to accommodate multiple datasets. The app enables users to visualize data containing various types of information simultaneously, facilitating comprehensive analysis. Additionally, it includes a user management system to regulate database accessibility for different users.
- [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/)
- [ShinyArchRUiO](https://github.com/EskelandLab/ShinyArchRUiO) - [R] - Shiny based web app for visualization of single-cell ATAC-seq data using ArchR. [ShinyArchR.UiO: user-friendly, integrative and open-source tool for visualization of single-cell ATAC-seq data using ArchR](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab680/6377776)
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