The repository includes all analysis necessary to arrive at the figures for the SPECTRUM TME paper.
Scripts are separated into preprocessing scripts and plotting scripts.
STATUS
- OPEN
- DONE
Processed expression data
(File paths on juno)
The output from Nick Ceglia's scRNA-seq pipeline serves as an input to the analysis.
- SPECTRUM v6 pre-Rx cohort expression object:
/work/shah/isabl_data_lake/analyses/68/75/6875/RNASCP/outs/
- SPECTRUM v6 pre-Rx cohort embedding table:
/work/shah/isabl_data_lake/analyses/68/75/6875/RNASCP/outs/cells.tsv
- v6 cell type objects (pipeline output, for annotated objects, see further below):
/work/shah/isabl_data_lake/analyses/68/75/6875/RNASCP/outs/{cell_type}.rds
- v6 cell type cluster markers:
/work/shah/isabl_data_lake/analyses/68/76/6875/RNASCP/outs/{cell_type}_markers.tsv
- SPECTRUM v7 pre-Rx cohort expression object:
/work/shah/isabl_data_lake/analyses/84/78/8478/RNASCP/outs/
- SPECTRUM v7 pre-Rx cohort embedding table:
/work/shah/isabl_data_lake/analyses/84/78/8478/RNASCP/outs/cells.tsv
- v7 cell type objects (pipeline output, for annotated objects, see further below):
/work/shah/isabl_data_lake/analyses/84/78/8478/RNASCP/outs/{cell_type}.rds
- v7 cell type cluster markers:
/work/shah/isabl_data_lake/analyses/84/78/8478/RNASCP/outs/{cell_type}_markers.tsv
Meta data
(File paths in this repo)
- scRNA-seq sample sheet:
- google spreadsheet owned by Ignacio
- downloaded copy, Dec 3rd, 2020: [
_data/small/MSK\ SPECTRUM\ -\ Single\ cell\ RNA-seq_v6.xlsx
](_data/small/MSK\ SPECTRUM\ -\ Single\ cell\ RNA-seq_v6.xlsx)
- color code:
_data/small/signatures/hgsc_v7_colors.yaml
- mutational signature consensus labels:
_data/small/mutational_signatures_summary_v3.tsv
Cohort
-
compute patient specificity from SNN graph
-
run consensusOV for TCGA subtype analysis
- helper script to start runs:
_preprocessing/020_SPECTRUM_freeze_v7_TCGA_signatures.R
- parameterized markdown to compute consensusOV for a given
patient.rds
input file_preprocessing/021_SPECTRUM_freeze_v7_TCGA_signatures_per_patient.Rmd
- summarized report of TCGA analysis
_preprocessing/022_SPECTRUM_freeze_v7_TCGA_summary.html
- helper script to start runs:
-
output files and objects:
- patient specificity per cell
- TCGA consensusOV:
/work/shah/uhlitzf/data/SPECTRUM/freeze/v7/consensusOV/SPECTRUM_freeze_v7_consensusOV.tsv
Cell type subsets
-
common tasks
- annotate sub type clusters and filter out doublet clusters
- run progeny for pathway scoring
- score gene signature modules
-
individual scripts for common tasks:
- B.super
_preprocessing/031_SPECTRUM_freeze_v7_prepro_B.super.Rmd
- Fibroblast.super
_preprocessing/032_SPECTRUM_freeze_v7_prepro_Fibroblast.super.Rmd
- T.super
_preprocessing/033_SPECTRUM_freeze_v7_prepro_T.super.Rmd
- Myeloid.super
_preprocessing/034_SPECTRUM_freeze_v7_prepro_Myeloid.super.Rmd
- Ovarian.cancer.cell.super
_preprocessing/035_SPECTRUM_freeze_v7_prepro_Ovarian.cancer.cell.super.Rmd
- Endothelial.super
_preprocessing/036_SPECTRUM_freeze_v7_prepro_Endothelial.super.Rmd
- B.super
-
cell type specific tasks
- Cancer cells: filter out low quality cells <1% mito reads and recluster
- T cells: subcluster CD8 T cells and run diffusion map on CD8 subset
- Myeloid cells: run diffusion map on macrophage subset
- major cell types
-
/work/shah/uhlitzf/data/SPECTRUM/freeze/v7/Ovarian.cancer.super_processed_filtered_annotated.rds
-
/work/shah/uhlitzf/data/SPECTRUM/freeze/v7/T.super_processed_filtered_annotated.rds
-
/work/shah/uhlitzf/data/SPECTRUM/freeze/v7/Myeloid.super_processed_filtered_annotated.rds
-
/work/shah/uhlitzf/data/SPECTRUM/freeze/v7/Fibroblast.super_processed_filtered_annotated.rds
-
B.super.annotated.rds
-
Endothelial.cell.super.annotated.rds
-
- subset objects
-
/work/shah/uhlitzf/data/SPECTRUM/freeze/v7/CD8.T_processed_filtered.rds
-
/work/shah/uhlitzf/data/SPECTRUM/freeze/v7/work/shah/uhlitzf/data/SPECTRUM/freeze/v7/DCs_processed.rds
-
/work/shah/uhlitzf/data/SPECTRUM/freeze/v7/work/shah/uhlitzf/data/SPECTRUM/freeze/v7/Macrophages_processed.rds
-
- supplementary marker tables
-
/work/shah/uhlitzf/data/SPECTRUM/freeze/v7/supplementary_tables/Ovarian.cancer.super_marker_table_annotated.tsv
-
/work/shah/uhlitzf/data/SPECTRUM/freeze/v7/supplementary_tables/T.super_marker_table_annotated_full.tsv
-
/work/shah/uhlitzf/data/SPECTRUM/freeze/v7/supplementary_tables/Myeloid.super_marker_table_annotated.tsv
-
/work/shah/uhlitzf/data/SPECTRUM/freeze/v7/supplementary_tables/Fibroblast.super_marker_table_annotated.tsv
-
Cohort (Fig 2)
110_cohort_plotting_umap_v7.html
- UMAP embeddings
- Patient specificity
- TCGA subtypes
115_cohort_plotting_composition_v7.html
- Composition barplots scRNA
- Composition barplots mpIF
Cancer cell (Fig 3)
120_cancer_cell_plotting_umap_v7.html
- UMAP embeddings
- Marker heatmap
- Composition barplots
- Pathway heatmap and boxplots
T cell (Fig 5)
130_T_cell_plotting_umap_comp_heatmap_v7.html
- UMAP embeddings
- Marker heatmap
- Composition barplots
135_T_cell_CD8_diffusion_v7.html
- DC embeddings
- Pseudotime trajectories
- Module boxplots
- Correlation scatter
Myeloid cell (Fig 6)
140_Myeloid_cell_plotting_umap_comp_heatmap_v7.html
- UMAP embeddings
- Marker heatmap
- Composition barplots
145_Macrophage_diffusion_v7.html
- UMAP marker gene embeddings
- Module score boxplots