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Co-authored-by: Ally Hawkins <[email protected]>
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sjspielman and allyhawkins authored Mar 6, 2024
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Expand Up @@ -143,7 +143,7 @@ Distributions reflect broad agreement between platforms in the total number of g


<!-- Figure S3 -->
![**Processing other sequencing modalities `scpca-nf`.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_s3.png?sanitize=true){#fig:figs3 tag="S3" width="7in"}
![**Processing other sequencing modalities with `scpca-nf`.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_s3.png?sanitize=true){#fig:figs3 tag="S3" width="7in"}

A. Overview of the bulk RNA-Seq workflow.
A set of FASTQ files from libraries sequenced with bulk RNA-seq are provided as input.
Expand All @@ -158,7 +158,7 @@ The workflow directly returns the results from running `spaceranger` without any

<!-- Figure S4 -->
![**Assessment of cell type annotation quality.**](https://raw.githubusercontent.com/AlexsLemonade/scpca-paper-figures/main/figures/compiled_figures/pngs/figure_s4.png?sanitize=true){#fig:figs4 tag="S4" width="7in"}
Both plots in this figure are examples of diagnostic plots in the cell type summary report, shown for library `SCPCL000001`.
Both plots in this figure are examples of diagnostic plots found in the cell type summary report, shown for library `SCPCL000001`.

A. Diagnostic plot showing `SingleR` cell type annotation quality.
Cell type annotations are shown on the y-axis, the _delta median_ statistic is shown on the x-axis.
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