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Copy file name to clipboardExpand all lines: README.Rmd
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[](https://codecov.io/gh/LieberInstitute/spatialLIBD?branch=master)
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Welcome to the `spatialLIBD` project! It is composed by a [shiny](https://shiny.rstudio.com/) web application at [jhubiostatistics.shinyapps.io/spatialLIBD/](https://jhubiostatistics.shinyapps.io/spatialLIBD/), a Bioconductor package at [bioconductor.org/packages/spatialLIBD](http://bioconductor.org/packages/spatialLIBD) (or from [here](http://research.libd.org/spatialLIBD/)), and a [research article](https://www.biorxiv.org/search/maynard%252Bcollado%252Bweber%252Bhicks%252Bmartinowich%252Bjaffe) with the scientific knowledge we drew from this dataset.
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Welcome to the `spatialLIBD` project! It is composed of:
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* a [shiny](https://shiny.rstudio.com/) web application that we are hosting at [jhubiostatistics.shinyapps.io/spatialLIBD/](https://jhubiostatistics.shinyapps.io/spatialLIBD/) that can handle a [limited](https://github.com/LieberInstitute/spatialLIBD/issues/2) set of concurrent users,
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* a Bioconductor package at [bioconductor.org/packages/spatialLIBD](http://bioconductor.org/packages/spatialLIBD) (or from [here](http://research.libd.org/spatialLIBD/)) that lets you analyze the data and run a local version of our web application (with our data or yours),
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* and a [research article](https://www.biorxiv.org/search/maynard%252Bcollado%252Bweber%252Bhicks%252Bmartinowich%252Bjaffe) with the scientific knowledge we drew from this dataset. The analysis code for our project is available [here](https://github.com/LieberInstitute/HumanPilot/).
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The web application allows you to browse the LIBD human dorsolateral pre-frontal cortex (DLPFC) spatial transcriptomics data generated with the 10x Genomics Visium platform. Through the [R/Bioconductor package](https://bioconductor.org/packages/spatialLIBD) you can also download the data as well as visualize your own datasets using this web application. Please check the [bioRxiv pre-print](https://www.biorxiv.org/search/maynard%252Bcollado%252Bweber%252Bhicks%252Bmartinowich%252Bjaffe) for more details about this project.
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If you tweet about this website, the data or the R package please use the <code>#spatialLIBD</code> hashtag. You can find previous tweets that way as shown <ahref="https://twitter.com/search?q=%23spatialLIBD&src=typed_query">here</a>. Thank you! <ahref="https://twitter.com/intent/tweet?button_hashtag=spatialLIBD&ref_src=twsrc%5Etfw"class="twitter-hashtag-button"data-show-count="false">Tweet #spatialLIBD</a><scriptasyncsrc="https://platform.twitter.com/widgets.js"charset="utf-8"></script>
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## Study design
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As a quick overview, the data presented here is from portion of the DLPFC that spans six neuronal layers plus white matter (**A**) for a total of three subjects with two pairs of spatially adjacent replicates (**B**). Each dissection of DLPFC was designed to span all six layers plus white matter (**C**). Using this web application you can explore the expression of known genes such as _SNAP25_ (**D**, a neuronal gene), _MOBP_ (**E**, an oligodendrocyte gene), and known layer markers from mouse studies such as _PCP4_ (**F**, a known layer 5 marker gene).
Through the `spatialLIBD` package you can access the processed data in it's final R format. However, we also provide a table of links so you can download the raw data we received from 10x Genomics.
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### Processed data
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Using `spatialLIBD` you can access the Human DLPFC spatial transcriptomics data from the 10x Genomics Visium platform. For example, this is the code you can use to access the layer-level data. For more details, check the help file for `fetch_data()`.
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citation('spatialLIBD')
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```
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Please note that the `spatialLIBD` was only made possible thanks to many other R and bioinformatics software authors. We have cited their work either in the pre-print or the vignette of the R package.
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