Merge branch 'main' into sjspielman/fig3-fig4-caption

content/100.figure-table-legends.md

@@ -21,7 +21,7 @@ A. An overview of `scpca-nf`, the primary workflow for processing single-cell an
 Mapping is first performed with `alevin-fry` to generate a gene-by-cell count matrix, which is read into `R` and converted into a `SingleCellExperiment` (`SCE`) object.
 This `SCE` object is exported as the `Unfiltered SCE Object` before further post-processing.
 Next, empty droplets are filtered out, and the resulting `SCE` is exported as the `Filtered SCE Object`.
-The filtered object undergoes additional post-processing, including filtering out low-quality cells, normalizing counts, and performing dimension reduction including principal components analysis and UMAP calculation.
+The filtered object undergoes additional post-processing, including removing low-quality cells, normalizing counts, and performing dimension reduction including principal components analysis and UMAP calculation.
 The object undergoes cell type annotation and is exported as the `Processed SCE Object`.
 A summary QC report and a supplemental cell type report are prepared and exported.
 Finally, all `SCE` files are converted to `AnnData` format and exported.
@@ -32,7 +32,6 @@ C. The number of genes detected in each cell passing the empty droplets filter a
 Points are colored by the percentage of mitochondrial reads in the cell.
 D. `miQC` model diagnostic plot showing the percent of mitochondrial reads in each cell against the number of genes detected in the `Filtered SCE Object`.
 Points are colored by the probability that the cell is compromised as determined by `miQC`.
-This plot is only present in summary QC reports whose libraries were filtered with `miQC`.
 E. The percent of mitochondrial reads in each cell against the number of genes detected in each cell.
 Points are colored by whether the cell was kept or removed, as determined by both `miQC` and a minimum unique gene count cutoff, prior to normalization and dimensionality reduction.
 F. UMAP embeddings of log-normalized RNA expression values where each cell is colored by the number of genes detected.