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v0.99.3 -- update all READMEs. Details at news.md
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lcolladotor committed Feb 27, 2020
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Package: spatialLIBD
Title: LIBD Visium spatial transcriptomics human pilot data inspector
Version: 0.99.2
Version: 0.99.3
Date: 2020-02-27
Authors@R:
c(
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6 changes: 6 additions & 0 deletions NEWS.md
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# spatialLIBD 0.99.3

* Further refine the READMEs (pkg and shiny). They now include the list of
links to the raw 10x Genomics files as well as a short description of the
project at the top. This was in response to feedback by Andrew Jaffe.

# spatialLIBD 0.99.2

* Update main package READMEs to reflect the changes to the shiny web app README.md.
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50 changes: 49 additions & 1 deletion README.Rmd
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[![Codecov test coverage](https://codecov.io/gh/LieberInstitute/spatialLIBD/branch/master/graph/badge.svg)](https://codecov.io/gh/LieberInstitute/spatialLIBD?branch=master)
<!-- badges: end -->

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.
Welcome to the `spatialLIBD` project! It is composed of:

* 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,
* 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),
* 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/).

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.

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 <a href="https://twitter.com/search?q=%23spatialLIBD&src=typed_query">here</a>. Thank you! <a href="https://twitter.com/intent/tweet?button_hashtag=spatialLIBD&ref_src=twsrc%5Etfw" class="twitter-hashtag-button" data-show-count="false">Tweet #spatialLIBD</a><script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>

## Study design

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).
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## Access the data

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.

### Processed data

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()`.

```{r 'access_data', message=FALSE, fig.height = 8, fig.width = 9}
Expand All @@ -100,6 +110,43 @@ sce_image_clus(
```


### Raw data

Below you can find the links to the raw data we received from 10x Genomics.

```{r 'AWS_links', eval = FALSE, echo = FALSE}
## Read in the table of links from the HumanPilot repository
## Since this depends on another repo, I set eval to FALSE.
aws_links <-
read.table(
'../HumanPilot/AWS_File_locations.tsv',
header = TRUE,
stringsAsFactors = FALSE
)
## Format into markdown links
for (i in seq_len(ncol(aws_links))[-1]) {
aws_links[[i]] <- paste0('[AWS](', aws_links[[i]], ')')
}
## Print the table
knitr::kable(aws_links, caption = 'Links to the Human DLPFC Visium raw data files', format = 'markdown')
```

| SampleID|h5_filtered |h5_raw |image_hi |image_lo |loupe |
|--------:|:-----------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------|
| 151507|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151507_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151507_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151507_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151507_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151507.cloupe) |
| 151508|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151508_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151508_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151508_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151508_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151508.cloupe) |
| 151509|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151509_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151509_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151509_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151509_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151509.cloupe) |
| 151510|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151510_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151510_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151510_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151510_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151510.cloupe) |
| 151669|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151669_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151669_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151669_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151669_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151669.cloupe) |
| 151670|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151670_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151670_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151670_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151670_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151670.cloupe) |
| 151671|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151671_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151671_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151671_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151671_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151671.cloupe) |
| 151672|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151672_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151672_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151672_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151672_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151672.cloupe) |
| 151673|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151673_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151673_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151673_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151673_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151673.cloupe) |
| 151674|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151674_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151674_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151674_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151674_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151674.cloupe) |
| 151675|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151675_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151675_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151675_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151675_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151675.cloupe) |
| 151676|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151676_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151676_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151676_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151676_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151676.cloupe) |


## Citation

Expand All @@ -110,6 +157,7 @@ run this yourself to check for any updates on how to cite __spatialLIBD__.
citation('spatialLIBD')
```

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.

## Code of conduct

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