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mdibl/scscape output

All Output Directories

Every output directory will always contain a .*Validation.log and .*Versions.log

  • .*Validation.log will contain essential information, paramaters set within the module, and updates to the Seurat Object.(ie. If PCs were automatically selected, the PC chosen will be shown here.)

  • .*Versions.log will contain all of the specific R pacakges and versions used for that module.

sampProcessing

Initial_SO

00_<sampleName>_InitialSO.rds: A barebones Seurat object with initial filtering of: - genes specified to be removed - genes expressed in fewer cells than set by the min_cells parameter - cells with fewer genes than set by the min_features parameter

Normalize_QC

01_<sampleName>_NormQCSO.rds: A Seurat object that contains cell cycle (unless otherwise specified in parameters) scores mitochondrial percentages. Additional filtering is done based on per-cell RNA counts, Gene counts, and mitocodrial percentages.

01_<sampleName>_preFilterQC.pdf: Plots showing cells before quality control filtering.

01_<sampleName>_postFilterQC.pdf: Plots showing cells after quality control filtering.

Doublet_Detection

02_<sampleName>_DoubletsRmSO.rds: A Seurat object with predicted doublets removed. 02_<sampleName>_ElbowPlot.pdf: Plot showing the the PC selected. 02_<sampleName>VisualizeDoublets.pdf: Plot showing the breakdown of singlets and doublets.

Analysis Groups (Segmentation)

Merge

03_<analysisGroup>_MergedSO.rds: A Seurat object containing multiple samples based on the segmentation.csv file. <anaysisGroup>postMergeQC.pdf: Plot showing post-qc filtering for all of the samples in the analysis group.

PCA

04_<analysisGroup>_PCASO.rds: A Seurat object that contains a principle component reduction slot with 1-100 PC coordiantes. 04_<analysisGroup>_Merged_ElbowPlot.pdf: Elbow plot of pc # vs. stdev marked with the selected PC cutoff. Rplots.pdf: findPC output elbow plot with associated metrics used to decide the pC cutoff (2nd derivative, 1st derivative, & preceding residual).

Integration

05_<analysisGroup>_IntegrateSO.rds: A Seurat object that has been run through Integration.

Nearest_Neighbors-Clusters

06_<analysisGroup>_ClusterSO.rds: A Seurat object that has been clustered for both integrated and unintegrated. <analysisGroup><Integrated/Unintegrated>SankeyPlot.pdf: A breakdown of the clusting across the spectrum of resolutions. marker/: A directory of marker genes for each cluster of each resolution for both Integrated and Unintegrated.

Dimensional_Reduction

08_<analysisGroup>_FinalSO.rds: A Seurat object with projections (both UMAP and TSNE) for integraged and unintegrated. <analysisGroup>.cloupe: A loupe file, built from the Seurat object, that can be directly opened in the 10X Loupe Browser Applicaiton. <analysisGroup><Integrated/Unintegrated><UMAP/TSNE>.pdf: Set of plots showing the projections with coloring based on various metadata columns.