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Merged
jashapiro merged 2 commits into from
Oct 17, 2025
Merged

Prevent unnecessary redownloads for vignettes #30

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7cb661a
Don't delete downloads for vignettes
jashapiro Oct 17, 2025
1191d92
update output
jashapiro Oct 17, 2025
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22 changes: 6 additions & 16 deletions vignettes/ScPCAr.Rmd
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Expand Up @@ -311,29 +311,19 @@ file_paths <- ScPCAr::download_sample(
destination = "scpca_data",
format = "sce"
)
```

```
## Downloading SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17.zip ...
```

```
## Unzipping to scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17...
```

``` r
# List the files that were downloaded
file_paths
```

```
## [1] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/README.md"
## [2] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/single_cell_metadata.tsv"
## [3] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/SCPCL000001_celltype-report.html"
## [4] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/SCPCL000001_filtered.rds"
## [5] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/SCPCL000001_processed.rds"
## [6] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/SCPCL000001_qc.html"
## [7] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/SCPCL000001_unfiltered.rds"
## [2] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/SCPCL000001_celltype-report.html"
## [3] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/SCPCL000001_filtered.rds"
## [4] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/SCPCL000001_processed.rds"
## [5] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/SCPCL000001_qc.html"
## [6] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/SCPCL000001_unfiltered.rds"
## [7] "scpca_data/SCPCS000001_SINGLE-CELL_SINGLE-CELL-EXPERIMENT_2025-10-17/single_cell_metadata.tsv"
```

## Understanding the downloaded file structure
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1 change: 1 addition & 0 deletions vignettes/ScPCAr.Rmd.orig
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Expand Up @@ -168,6 +168,7 @@ The function will download and unpack the files associated with that sample, and
Let's start with SingleCellExperiment format:

```{r download-sce}
#| message: FALSE
# Download SingleCellExperiment data for our sample
# This will create a directory structure under "scpca_data/"
file_paths <- ScPCAr::download_sample(
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1 change: 0 additions & 1 deletion vignettes/precompile.R
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Expand Up @@ -9,7 +9,6 @@
devtools::load_all()

# Pre-compiled vignettes that depend on data downloads
unlink(here::here("vignettes/scpca_data"), recursive = TRUE)
knitr::knit(here::here("vignettes/ScPCAr.Rmd.orig"), output = here::here("vignettes/ScPCAr.Rmd"))

# move figures
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