Draft edits

content/01.abstract.md

@@ -1,15 +1,15 @@
 ## Abstract {.page_break_before}
 
-The Single-cell Pediatric Cancer Atlas (ScPCA) Portal (https://scpca.alexslemonade.org/) is a data resource for uniformly processed single-cell and single-nuclei RNA sequencing (RNA-seq) data and de-identified metadata from pediatric tumor samples. 
+The Single-cell Pediatric Cancer Atlas (ScPCA) Portal (https://scpca.alexslemonade.org/) is a data resource for uniformly processed single-cell and single-nuclei RNA sequencing (RNA-seq) data and de-identified metadata from pediatric tumor samples.
 Originally comprised of data from 10 projects funded by Alex’s Lemonade Stand Foundation, the Portal currently contains summarized gene expression data for over 500 samples from over 50 types of cancers from ALSF-funded and community-contributed datasets.
 In addition to gene expression data from single-cell and single-nuclei RNA-seq, the Portal holds data obtained from bulk RNA-seq, spatial transcriptomics, and feature barcoding methods, such as CITE-seq and cell hashing. 
 
 ScPCA data are available for download as `SingleCellExperiment` or `AnnData` objects and are ready for downstream analyses.
-Objects include raw counts and normalized gene expression data, PCA and UMAP coordinates, and cell type annotations. 
-Additionally, all downloads include two summary reports for each library: a quality control report summarizing sample statistics and displaying visualizations of cell metrics and a cell type annotation report with comparisons among cell type annotation methods and diagnostic plots to assess annotation quality. 
-Merged `SingleCellExperiment` and `AnnData` objects containing all gene expression data and metadata for all samples in an ScPCA project are also available for download. 
-These objects are useful when performing analysis on multiple samples simultaneously. 
+Objects include raw counts and normalized gene expression data, PCA and UMAP coordinates, and automated cell type annotations.
+Additionally, all downloads include two summary reports for each library: a quality control report summarizing sample statistics and displaying visualizations of cell metrics and a cell type annotation report with comparisons among cell type annotation methods and diagnostic plots to assess annotation quality.
+Merged `SingleCellExperiment` and `AnnData` objects containing all gene expression data and metadata for all samples in an ScPCA project are also available for download.
+These objects are useful when performing analysis on multiple samples simultaneously.
 Comprehensive documentation about data processing and the contents of files on the Portal, including a guide to getting started working with an ScPCA dataset, can be found at <http://scpca.readthedocs.io>. 
 
-All data on the Portal were uniformly processed using `scpca-nf`, an open-source and efficient Nextflow workflow that uses `alevin-fry` to quantify all single-cell and single-nuclei RNA-seq data, any associated CITE-seq or cell hash data, spatial transcriptomics data, and bulk RNA-seq. 
+All data on the Portal were uniformly processed using `scpca-nf`, an open-source and efficient Nextflow workflow that uses `alevin-fry` to quantify all single-cell and single-nuclei RNA-seq data, any associated CITE-seq or cell hash data, spatial transcriptomics data, and bulk RNA-seq.
 Any pediatric cancer-relevant data sets processed with `scpca-nf` are eligible for inclusion on the ScPCA Portal, enabling continuous growth of the ScPCA Portal to help pediatric cancer researchers spend less time finding and processing data and more time answering their pressing research questions.

content/02.introduction.md

@@ -19,16 +19,16 @@ Thus, it is imperative to provide harmonized data from pediatric tumors to all p
 To address this unmet need, Alex's Lemonade Stand Foundation and the Childhood Cancer Data Lab developed and maintain the Single-cell Pediatric Cancer Atlas (ScPCA) Portal (https://scpca.alexslemonade.org/), an open-source data resource for single-cell and single-nuclei RNA-seq data of pediatric tumors.
 
 The ScPCA Portal holds uniformly processed summarized gene expression from 10X Genomics' droplet-based single-cell and single-nuclei RNA-seq for over 500 samples from a diverse set of over 50 types of pediatric cancers.
-Originally comprising data from 10 projects funded by Alex's Lemonade Stand Foundation, the Portal has since expanded to include data contributed by pediatric cancer research community members.
+Originally comprised of data from ten projects funded by Alex's Lemonade Stand Foundation, the Portal has since expanded to include data contributed by pediatric cancer research community members.
 In addition to gene expression data from single-cell and single-nuclei RNA-seq, the Portal includes data obtained from bulk RNA-seq, spatial transcriptomics, and feature barcoding methods, such as CITE-seq and cell hashing.
 All data provided on the portal are available in formats ready for downstream analysis as `SingleCellExperiment` or `AnnData` objects containing normalized gene expression counts, dimensionality reduction results, and cell type annotations.
 
 To ensure that all current and future data on the Portal are uniformly processed, we created `scpca-nf`, a Nextflow-based open-source pipeline (https://github.com/AlexsLemonade/scpca-nf).
 Using a consistent pipeline for all data increases transparency and allows users to perform analysis across multiple samples and projects without having to do any re-processing.
 The `scpca-nf` workflow uses `alevin-fry` [@doi:10.1038/s41592-022-01408-3] for fast and efficient quantification of gene expression for all samples on the Portal, including single-cell RNA-seq data and any associated CITE-seq or cell hash data, spatial transcriptomics data, and bulk RNA-seq data.
-The `scpca-nf` pipeline also serves as a resource for the community, allowing others to process their own samples for comparison to samples available on the Portal and allowing us to accept uniformly processed community contributions.
+The `scpca-nf` pipeline also serves as a resource for the community, allowing others to process their own samples for comparison to samples available on the Portal and submit uniformly processed community contributions to the Portal.
 
 Here, we present the Single-cell Pediatric Cancer Atlas as a resource for all pediatric cancer researchers.
 The ScPCA Portal provides downloads ready for immediate use, allowing researchers to skip time-consuming data re-processing and wrangling steps.
 We provide comprehensive documentation about data processing and the contents of files on the portal, including a guide to getting started working with an ScPCA dataset (https://scpca.readthedocs.io/).
-The ScPCA Portal helps advance pediatric cancer research by accelerating researchers' ability to answer important biological questions.
+The ScPCA Portal advances pediatric cancer research by accelerating researchers' ability to answer important biological questions.