nasqar / seuratwizard

This is a web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat.

NASQAR (Nucleic Acid SeQuence Analysis Resource):

A web-based platform for High-throughput sequencing data analysis and visualization

• Pre-print: NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization
• This repo contains the source code for the NASQAR homepage http://nasqar.abudhabi.nyu.edu/
• Below are links to github repos for the apps contained in NASQAR
• The Dockerfile can be used to build the latest image of NASQAR
• The latest Docker image for nasqar is available via DockerHub https://hub.docker.com/r/aymanm/nasqarall

Run using docker (Recommended):

Make sure Docker (version >= 17.03.0-ce) is installed.

docker run -p 80:80 aymanm/nasqarall:nasqar

This will run on port 80

To run on a different port:

docker run -p 8083:80 aymanm/nasqarall:nasqar

This will run on port 8083

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Apps included in NASQAR

NASQAR Custom apps:

• SeuratV3Wizard (scRNA)
• SeuratWizard (scRNA)
• deseq2shiny (Bulk RNA)
• GeneCountMerger (Pre-processing)
• ClusterProfShinyGSEA (Enrichment)
• ClusterProfShinyORA (Enrichment)

Other open-source apps:

• STARTapp
• DEApp
• Shaman

seuratwizard's Issues

perplexity for smaller dataset

Hi,

In RunTSNE function, perplexity=30 is always used. However, it might not be appropriate for smaller dataset, such as smart-Seq2 with less than 100 cells after filtering. Is it possible for you to dynamically assign perplexity value according to cell numbers?

Thanks,
Ge

cell browser export as the last step?

Hi, great tool! You may want to consider one day the automated created of a single cell browser, see cellbrowser.readthedocs.org or cells.ucsc.edu.

how to run it with docker file

how to run it with docker file

Plan to support Seurat v3

Many thanks for such neat package. I am just wondering whether you have any plan to support Seurat v3, considering the huge difference between v2 and v3. Of course, Seurat v3 is not officially released yet.

Best,
Ge

RunTSNE: do.fast is no longer used

Hi,

Regarding RunTSNE, it also makes senses to use multi threads. Something like

pbmc <- RunTSNE(object = pbmc, dims.use = input$tsnePCDim1:input$tsnePCDim2,
                      tsne.method="Rtsne",
                      num_threads=parallel::detectCores()/2)

error

HI,
when I try to run the example dataset it gives an error:
Warning: Error in CreateSeuratObject: unused arguments (raw.data = rawData, min.genes = input$mingenes)
93: eval [server-initInputData.R#207]
92: eval
91: withProgress
90: eventReactiveHandler [server-initInputData.R#197]
46: initSeuratObjReactive
45: [server-initInputData.R#190]
2: shiny::runApp
1: SeuratWizard
Kindly help.