Workflow: Single-Cell Differential Abundance Analysis

Fetched 2025-02-26 07:01:34 GMT

Single-Cell Differential Abundance Analysis Compares the composition of cell types between two tested conditions

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Inputs

ID Type Title Doc
alias String Analysis name
ranges String (Optional) Minimum and maximum thresholds for differential abundance scores

Minimum and maximum thresholds to filter out cells with the low (by absolute values) differential abundance scores. Can be set in a form of a comma- or space-separated list. Default: calculated based on the permutation test.

groupby String Grouping category (cluster, cell type, etc.)

Single cell metadata column to group cells by categories, such as clusters, cell types, etc., when generating UMAP and composition plots. Custom groups can be defined based on any single cell metadata added through the \"Datasets metadata (optional)\" or \"Selected cell barcodes (optional)\" inputs.

splitby String Comparison category

Single cell metadata column to split cells into two comparison groups before running differential abundance analysis. To split cells by dataset, use \"dataset\". Custom groups can be defined based on any single cell metadata added through the \"Datasets metadata (optional)\" or \"Selected cell barcodes (optional)\" inputs. The direction of comparison is always \"Second comparison group\" vs \"First comparison group\".

threads Number of cores/cpus to use

Parallelization parameter to define the number of cores/CPUs that can be utilized simultaneously. Default: 4

dimensions Integer (Optional) Dimensionality to be used when running differential abundance analysis (from 1 to 50)

Dimensionality to be used when running differential abundance analysis with DAseq (from 1 to 50). Default: 10

first_cond String First comparison group

Value from the single cell metadata column selected in \"Comparison category\" input to define the first group of cells for differential abundance analysis.

color_theme Color theme for all generated plots

Color theme for all generated plots. One of gray, bw, linedraw, light, dark, minimal, classic, void. Default: classic

second_cond String Second comparison group

Value from the single cell metadata column selected in \"Comparison category\" input to define the second group of cells for differential abundance analysis.

barcodes_data File (Optional) Selected cell barcodes (optional)

A TSV/CSV file to optionally prefilter the single cell data by including only the cells with the selected barcodes. The provided file should include at least one column named \"barcode\", with one cell barcode per line. All other columns, except for \"barcode\", will be added to the single cell metadata loaded from \"Single-cell Analysis with Clustered RNA/ATAC-Seq or WNN Datasets\" and can be utilized in the current or future steps of the analysis.

query_data_rds File Single-cell Analysis with Clustered RNA/ATAC-Seq or WNN Datasets

Analysis that includes single-cell multiome RNA and ATAC-Seq or just RNA-Seq datasets run through either \"Single-Cell Manual Cell Type Assignment\", \"Single-Cell RNA-Seq Cluster Analysis\", \"Single-Cell ATAC-Seq Cluster Analysis\", or \"Single-Cell WNN Cluster Analysis\" at any of the processing stages.

query_reduction Dimensionality reduction

Dimensionality reduction to be used for generating UMAP plots.

datasets_metadata File (Optional) Datasets metadata (optional)

If the selected single-cell analysis includes multiple aggregated datasets, each of them can be assigned to a separate group by one or multiple categories. This can be achieved by providing a TSV/CSV file with \"library_id\" as the first column and any number of additional columns with unique names, representing the desired grouping categories.

export_loupe_data Boolean (Optional) Save raw counts to Loupe file. I confirm that data is generated by 10x technology and accept the EULA available at https://10xgen.com/EULA

Save raw counts from the RNA assay to Loupe file. By enabling this feature you accept the End-User License Agreement available at https://10xgen.com/EULA. Default: false

export_html_report Boolean (Optional) Show HTML report

Export tehcnical report in HTML format. Default: true

Steps

ID Runs Label Doc
da_cells
../tools/sc-rna-da-cells.cwl (CommandLineTool)
Single-Cell Differential Abundance Analysis

Single-Cell Differential Abundance Analysis

Compares the composition of cell types between two tested conditions

compress_pdf_plots
../tools/tar-compress.cwl (CommandLineTool)
TAR compress

TAR compress =========================================

Creates compressed TAR file from a folder

Outputs

ID Type Label Doc
pdf_plots File Compressed folder with all PDF plots

Compressed folder with all PDF plots.

seurat_data_rds File Seurat object in RDS format

Seurat object. RDS format.

seurat_data_scope File (Optional) Seurat object in SCope compatible loom format

Seurat object. SCope compatible. Loom format.

ucsc_cb_html_data Directory (Optional) UCSC Cell Browser (data)

UCSC Cell Browser html data.

ucsc_cb_html_file File (Optional) UCSC Cell Browser

UCSC Cell Browser html index.

da_cells_human_log File Human readable error log

Human readable error log from the da_cells step.

da_cells_stderr_log File Error log

Stderr log from the da_cells step.

da_cells_stdout_log File Output log

Stdout log from the da_cells step.

sc_report_html_file File (Optional) Analysis log

Tehcnical report. HTML format.

rank_da_scr_plot_png File (Optional) Estimated thresholds for differential abundance score (all cells)

Estimated thresholds for differential abundance score. All cells. PNG format.

umap_gr_tst_plot_png File (Optional) UMAP colored by tested condition (downsampled)

UMAP colored by tested condition. First downsampled to the smallest dataset, then downsampled to the smallest tested condition group. PNG format.

seurat_rna_data_cloupe File (Optional) Seurat object in Loupe format

Seurat object. RNA counts. Loupe format.

umap_da_scr_cnt_plot_png File (Optional) UMAP colored by differential abundance score (all cells, continuous scale)

UMAP colored by differential abundance score, continuous scale. All cells. PNG format.

umap_da_scr_ctg_plot_png File (Optional) UMAP colored by differential abundance score (all cells, categorical scale)

UMAP colored by differential abundance score, categorical scale. All cells; categories are defined based on the selected ranges for the differential abundance score. PNG format.

cmp_gr_clst_spl_tst_plot_png File (Optional) Composition plot colored by cluster (split by tested condition, downsampled)

Composition plot colored by cluster. Split by tested condition; first downsampled to the smallest dataset, then downsampled to the smallest tested condition group. PNG format.

cmp_gr_tst_spl_clst_plot_png File (Optional) Composition plot colored by tested condition (split by cluster, downsampled)

Composition plot colored by tested condition. Split by cluster; first downsampled to the smallest dataset, then downsampled to the smallest tested condition group. PNG format.

umap_gr_clst_spl_tst_plot_png File (Optional) UMAP colored by cluster (split by tested condition, downsampled)

UMAP colored by cluster. Split by tested condition; first downsampled to the smallest dataset, then downsampled to the smallest tested condition group. PNG format.

cmp_bp_gr_tst_spl_clst_plot_png File (Optional) Composition box plot colored by tested condition (split by cluster, downsampled)

Composition box plot colored by tested condition. Split by cluster; downsampled to the smallest dataset. PNG format.

html json turtle jsonld rdfxml svg png dot zip ro yaml raw
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