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MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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About MultiQC

This report was generated using MultiQC, version 1.35

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MultiQC is published in Bioinformatics:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

MultiQC is developed by Seqera.

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

This report has been generated by the STAPLE analysis pipeline.

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Report generated on 2026-07-10, 12:07 EDT based on data in: /usr/local/scratch/dlvovs/work/9a/ffbe0a9767491de11e11aa5f6628c4

Sample Sheet

The sample sheet provided as input to the pipeline.

Showing ⁶/₆ rows and ⁸/₈ columns.

sample	data_directory	patient	year_born	gender	timepoint	timepoint_date	sample_type
T0-0078011	/local/projects-t3/fertig_staple/osteosarc/xenium/T0/output-XETG00279__0078011__B3__20260211__182948	XETG00279	1979	male	T0	2022-11	resection
T0-0078018	/local/projects-t3/fertig_staple/osteosarc/xenium/T0/output-XETG00279__0078018__C3__20260211__182947	XETG00279	1979	male	T0	2022-11	resection
T1-0102917	/local/projects-t3/fertig_staple/osteosarc/xenium/20260513__172829__jw_batch2/output-XETG00279__0102917__Region_1__20260513__172840	XETG00279	1979	male	T1	2024-06	re-resection
T2-0102913	/local/projects-t3/fertig_staple/osteosarc/xenium/20260513__172829__jw_batch2/output-XETG00279__0102913__Region_1__20260513__172841	XETG00279	1979	male	T2	2025-01	biopsy
T3-0103076	/local/projects-t3/fertig_staple/osteosarc/xenium/20260515__160744__jw_batch3/output-XETG00279__0103076__Region_1__20260515__160758	XETG00279	1979	male	T3	2025-04	resection
T3-0103350	/local/projects-t3/fertig_staple/osteosarc/xenium/20260515__160744__jw_batch3/output-XETG00279__0103350__Region_1__20260515__160758	XETG00279	1979	male	T3	2025-04	resection

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: samplesheet-section-plot_table

Sort	Column	Description	ID
\|\|	data_directory	data_directory	`data_directory`
\|\|	expression_profile	expression_profile	`expression_profile`
\|\|	patient	patient	`patient`
\|\|	year_born	year_born	`year_born`
\|\|	gender	gender	`gender`
\|\|	timepoint	timepoint	`timepoint`
\|\|	timepoint_date	timepoint_date	`timepoint_date`
\|\|	sample_type	sample_type	`sample_type`

Atlas Summary

Summary of the cells and genes in the atlas.

Showing ¹/₁ rows and ⁶/₆ columns.

Sample	n_genes	n_cells	mean_genes_by_counts	mean_cells_by_counts	mean_total_nnz_counts	mean_percent_mito
072925_IPISRC044_T1_T2_T3_sobj_merged_processed_tcr_bcr_mutMap_tcMap_annot_final	29264	28046	3030.4	2904.3	3.7	2.2

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: atlas-section-plot_table

Sort	Column	Description	ID
\|\|	n_genes	n_genes	`n_genes`
\|\|	n_cells	n_cells	`n_cells`
\|\|	mean_genes_by_counts	mean_genes_by_counts	`mean_genes_by_counts`
\|\|	mean_cells_by_counts	mean_cells_by_counts	`mean_cells_by_counts`
\|\|	mean_total_nnz_counts	mean_total_nnz_counts	`mean_total_nnz_counts`
\|\|	mean_percent_mito	mean_percent_mito	`mean_percent_mito`

Atlas Cell Types

Summary of the cell types in the atlas.

Showing ¹/₁ rows and ⁵/₅ columns.

Sample	Lymphoid	Myeloid	Tumor	Junk	Non_immune
072925_IPISRC044_T1_T2_T3_sobj_merged_processed_tcr_bcr_mutMap_tcMap_annot_final	15182	6066	3425	1979	1394

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: atlas_ct-section-plot_table

Sort	Column	Description	ID
\|\|	Lymphoid	Lymphoid	`Lymphoid`
\|\|	Myeloid	Myeloid	`Myeloid`
\|\|	Tumor	Tumor	`Tumor`
\|\|	Junk	Junk	`Junk`
\|\|	Non_immune	Non_immune	`Non_immune`

Input Summary

Summary of the AnnData object right after it was read.

Showing ⁶/₆ rows and ⁶/₆ columns.

Sample	n_genes	n_cells	mean_genes_by_counts	mean_cells_by_counts	mean_total_nnz_counts
T0-0078011	428	318320	41.8	31100.9	5.0
T0-0078018	428	426526	54.9	54710.1	4.7
T1-0102917	428	34478	81.0	6526.3	4.1
T2-0102913	428	122202	69.1	19715.5	3.0
T3-0103076	428	273156	26.5	16883.9	2.7
T3-0103350	428	201503	32.1	15100.1	3.0

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: adata-section-plot_table

Sort	Column	Description	ID
\|\|	n_genes	n_genes	`n_genes`
\|\|	n_cells	n_cells	`n_cells`
\|\|	mean_genes_by_counts	mean_genes_by_counts	`mean_genes_by_counts`
\|\|	mean_cells_by_counts	mean_cells_by_counts	`mean_cells_by_counts`
\|\|	mean_total_nnz_counts	mean_total_nnz_counts	`mean_total_nnz_counts`
\|\|	mean_percent_mito	mean_percent_mito	`mean_percent_mito`

Output Cell Types

Assigned cell types based on deconvolution / cell typing results. Unassigned counts appear in a nameless column.

Showing ⁶/₆ rows and ⁶/₆ columns.

Sample	Tumor		Non immune	Myeloid	Junk	Lymphoid
T0-0078011	149648	143692	13047	8700	1979	1254
T0-0078018	256695	130366	11439	22773	3467	1786
T1-0102917	23551	6728	1039	2746	145	269
T2-0102913	54952	40657	2411	13911	4733	5538
T3-0103076	42492	202118	1068	14276	4840	8362
T3-0103350	42764	133162	796	12072	5533	7176

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: deconvolved_ct-section-plot_table

Sort	Column	Description	ID
\|\|	Tumor	Tumor	`Tumor`
\|\|			`mqc_`
\|\|	Non immune	Non immune	`Non_immune`
\|\|	Myeloid	Myeloid	`Myeloid`
\|\|	Junk	Junk	`Junk`
\|\|	Lymphoid	Lymphoid	`Lymphoid`

Cell Type Probabilities

Average max cell type probabilities used to assign the cell types (greater is better).

Showing ⁶/₆ rows and ⁵/₅ columns.

Sample	Junk	Lymphoid	Myeloid	Non immune	Tumor
T0-0078011	0.5	0.7	0.6	0.7	0.9
T0-0078018	0.5	0.6	0.6	0.6	0.9
T1-0102917	0.6	0.7	0.7	0.7	0.9
T2-0102913	0.6	0.6	0.7	0.7	0.8
T3-0103076	0.6	0.6	0.7	0.7	0.8
T3-0103350	0.6	0.6	0.7	0.7	0.8

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: deconvolved_probs-section-plot_table

Sort	Column	Description	ID
\|\|	Junk	Junk	`Junk`
\|\|	Lymphoid	Lymphoid	`Lymphoid`
\|\|	Myeloid	Myeloid	`Myeloid`
\|\|	Non immune	Non immune	`Non_immune`
\|\|	Tumor	Tumor	`Tumor`

Average Clustering

This graph measure shows the degree to which nodes cluster together.

Showing ⁶/₆ rows and ⁶/₆ columns.

Sample Name	Junk	Lymphoid	Myeloid	Non immune	Tumor	NA
T0-0078011	0.5	0.5	0.4	0.4	0.4	0.4
T0-0078018	0.5	0.5	0.5	0.5	0.4	0.5
T1-0102917	0.4	0.4	0.4	0.5	0.4	0.4
T2-0102913	0.4	0.4	0.4	0.4	0.4	0.5
T3-0103076	0.4	0.4	0.4	0.4	0.4	0.4
T3-0103350	0.4	0.4	0.4	0.4	0.4	0.4

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: average_clustering-section-plot_table

Sort	Column	Description	ID
\|\|	Junk	Junk	`Junk`
\|\|	Lymphoid	Lymphoid	`Lymphoid`
\|\|	Myeloid	Myeloid	`Myeloid`
\|\|	Non immune	Non immune	`Non_immune`
\|\|	Tumor	Tumor	`Tumor`
\|\|	NA	NA	`NA`

Closeness Centrality

This graph measure reflects how close the group is to other nodes.

Showing ⁶/₆ rows and ⁶/₆ columns.

Sample Name	Junk	Lymphoid	Myeloid	Non immune	Tumor	NA
T0-0078011	0.2	0.1	0.3	0.3	0.6	0.6
T0-0078018	0.1	0.1	0.3	0.2	0.7	0.5
T1-0102917	0.1	0.2	0.5	0.3	1.3	0.4
T2-0102913	0.2	0.3	0.4	0.2	0.3	0.6
T3-0103076	0.4	0.6	0.5	0.3	0.5	0.8
T3-0103350	0.4	0.5	0.5	0.2	0.6	0.7

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: closeness_centrality-section-plot_table

Sort	Column	Description	ID
\|\|	Junk	Junk	`Junk`
\|\|	Lymphoid	Lymphoid	`Lymphoid`
\|\|	Myeloid	Myeloid	`Myeloid`
\|\|	Non immune	Non immune	`Non_immune`
\|\|	Tumor	Tumor	`Tumor`
\|\|	NA	NA	`NA`

Co Occurrence

Co Occurrence mean of Co-occurrence of cell types across samples. Values greater than 1 indicate that the cell type is found near other cell types more than average at a given distance.

Created with MultiQC

Degree Centrality

This graph measure is the fraction of non-group members connected to group members.

Showing ⁶/₆ rows and ⁶/₆ columns.

Sample Name	Junk	Lymphoid	Myeloid	Non immune	Tumor	NA
T0-0078011	0.0	0.0	0.1	0.1	0.4	0.6
T0-0078018	0.0	0.0	0.2	0.1	0.6	0.5
T1-0102917	0.0	0.0	0.3	0.1	0.6	0.3
T2-0102913	0.2	0.2	0.4	0.1	0.4	0.5
T3-0103076	0.1	0.1	0.2	0.0	0.2	0.8
T3-0103350	0.1	0.2	0.2	0.0	0.3	0.7

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: degree_centrality-section-plot_table

Sort	Column	Description	ID
\|\|	Junk	Junk	`Junk`
\|\|	Lymphoid	Lymphoid	`Lymphoid`
\|\|	Myeloid	Myeloid	`Myeloid`
\|\|	Non immune	Non immune	`Non_immune`
\|\|	Tumor	Tumor	`Tumor`
\|\|	NA	NA	`NA`

Squidpy Ligrec Interactions

Top 100 mean interactions across samples shown as no groups were specified in the sample sheet.

Created with MultiQC

Moran I Interactions

Top 100 mean interactions across samples shown as no groups were specified in the sample sheet.

Created with MultiQC

Spatial Neighbors

Cell type immediate neighborhood across samples. The rate of self-neighborhood indicates clustering of a cell type. The rate of neighbors with other cell types (self omitted) indicates how these clusters interact with each other.

Created with MultiQC

Software Versions

Software Versions lists versions of software tools extracted from file contents.

Group	Software	Version
ADATA_ADD_METADATA	anndata	`0.12.11`
ADATA_FROM_XENIUM	spatialdata_io	`0.6.0`
	squidpy	`1.8.1`
ATLAS_GET	boto3	`1.42.93`
	requests	`2.33.1`
ATLAS_MATCH	anndata	`0.12.11`
	numpy	`2.4.4`
QC	anndata	`0.12.11`
	pandas	`2.3.3`
RCTD	Matrix	`1.7-4`
	R	`4.5.3`
	reticulate	`1.45.0`
	spacexr	`2.2.1`
SQUIDPY_LIGREC_ANALYSIS	anndata	`0.12.10`
	scanpy	`1.11.5`
	squidpy	`1.6.6.dev24+g32789aefd`
SQUIDPY_SPATIAL_PLOTS	anndata	`0.12.10`
	numpy	`2.4.3`
	python	`3.11.15`
	squidpy	`1.6.6.dev24+g32789aefd`
STAPLE_XSAMPLE	anndata	`0.12.10`
	json	`2.0.9`
	numpy	`2.4.3`
	pandas	`2.3.3`
	scipy	`1.17.1`
Workflow	Nextflow	`26.04.1`
	STAPLE	`v2.3.0-g2c78896`

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