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Add singleCellTK and alphabetize web portals and apps section
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dfjenkins3 authored and seandavi committed May 23, 2018
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Expand Up @@ -186,12 +186,13 @@ List of software packages (and the people developing these methods) for single-c
- [Ginkgo](http://qb.cshl.edu/ginkgo) - [R, C] - Ginkgo is a web application for single-cell copy-number variation analysis and visualization.
- [Granatum](http://garmiregroup.org/granatum/app) - Granatum 🍇 is a graphical single-cell RNA-seq (scRNA-seq) analysis pipeline for genomics scientists. [Published in December 2017](https://doi.org/10.1186/s13073-017-0492-3).
- [JingleBells](http://jinglebells.bgu.ac.il/) - A repository of standardized single cell RNA-Seq datasets for analysis and visualization in IGV at the single cell level. Currently focused on immune cells (http://www.jimmunol.org/content/198/9/3375.long).
- [Single Cell Portal](https://portals.broadinstitute.org/single_cell) - The Single-Cell Portal was developed to facilitate open data and open science in Single-cell Genomics. The portal currently focuses on sharing scientific results interactively, and sharing associated datasets.
- [SAKE](http://sake.mhammell.tools/) - Single-cell RNA-Seq Analysis and Clustering Evaluation.
- [scmap](http://www.hemberg-lab.cloud/scmap/) - A web tool for fast and accurate mapping of cells to a reference database using scRNA-seq data
- [SCPortalen](http://single-cell.clst.riken.jp/) - SCPortalen: human and mouse single-cell centric database. [ref](https://doi.org/10.1093/nar/gkx949)
- [scRNA.seq.datasets](https://hemberg-lab.github.io/scRNA.seq.datasets) - Collection of public scRNA-Seq datasets used by [Hemberg Lab](http://www.sanger.ac.uk/science/groups/hemberg-group)
- [scRNASeqDB](https://bioinfo.uth.edu/scrnaseqdb/) - A database aggregating human single-cell RNA-seq datasets. [ref](http://biorxiv.org/content/early/2017/01/31/104810)
- [SCPortalen](http://single-cell.clst.riken.jp/) - SCPortalen: human and mouse single-cell centric database. [ref](https://doi.org/10.1093/nar/gkx949)
- [Single Cell Portal](https://portals.broadinstitute.org/single_cell) - The Single-Cell Portal was developed to facilitate open data and open science in Single-cell Genomics. The portal currently focuses on sharing scientific results interactively, and sharing associated datasets.
- [singleCellTK](https://bioconductor.org/packages/release/bioc/html/singleCellTK.html) - The singleCellTK is an R/Shiny package and GUI for analyzing and visualizing scRNA-Seq through a web interface. Analysis modules include data summary and filtering, dimensionality reduction and clustering, batch correction, differential expression analysis, pathway activity analysis, and power analysis.

## Journal articles of general interest

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