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v0.99.10 -- update AWS file locations, resolve a bug on Windows repor…
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…ted by http://bioconductor.org/spb_reports/spatialLIBD_buildreport_20200302120158.html#tokay2_buildsrc_anchor
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@lcolladotor
lcolladotor committed Mar 3, 2020
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Package: spatialLIBD
Title: LIBD Visium spatial transcriptomics human pilot data inspector
Version: 0.99.9
Date: 2020-02-29
Version: 0.99.10
Date: 2020-03-03
Authors@R:
c(
person("Leonardo", "Collado-Torres", role = c("aut", "cre"),
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12 changes: 12 additions & 0 deletions NEWS.md
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# spatialLIBD 0.99.10

* Include AWS links to the image TIFF files (~500mb each) as requested by
Qian Zhu <[email protected]> for visualizing the data on the Giotto
Viewer https://www.biorxiv.org/content/10.1101/701680v1.

BUG FIXES

* Fix `fetch_data()` and the vignette by specifying the `mode = "wb"` for
`utils::download.file()` in order to resolve an issue with Windows OS reported
here http://bioconductor.org/spb_reports/spatialLIBD_buildreport_20200302120158.html#tokay2_buildsrc_anchor.

# spatialLIBD 0.99.9

* Link to https://doi.org/10.1101/2020.02.28.969931 now that its
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5 changes: 4 additions & 1 deletion R/fetch_data.R
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Expand Up @@ -105,7 +105,10 @@ fetch_data <-
dir.create(destdir,
showWarnings = FALSE,
recursive = TRUE)
utils::download.file(url, destfile = file_path, quiet = TRUE)
utils::download.file(url,
destfile = file_path,
quiet = TRUE,
mode = 'wb')
}
}

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28 changes: 14 additions & 14 deletions README.Rmd
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Expand Up @@ -139,20 +139,20 @@ for (i in seq_len(ncol(aws_links))[-1]) {
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) |
| SampleID|h5_filtered |h5_raw |image_full |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_full_image.tif) |[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_full_image.tif) |[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_full_image.tif) |[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_full_image.tif) |[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_full_image.tif) |[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_full_image.tif) |[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_full_image.tif) |[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_full_image.tif) |[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_full_image.tif) |[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_full_image.tif) |[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_full_image.tif) |[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_full_image.tif) |[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) |


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