MultiQC Report

Toolbox

MultiQC Toolbox

Highlight Samples

Regex mode off

Rename Samples

Click here for bulk input.

Paste two columns of a tab-delimited table here (eg. from Excel).

First column should be the old name, second column the new name.

Regex mode off

Show / Hide Samples

Regex mode off

Explain with AI

Configure AI settings to get explanations of plots and data in this report.

Anonymize samples off

Aspect ratio

Plot scaling

Download the raw data used to create the plots in this report below:

Format:

Note that additional data was saved in multiqc_data when this report was generated.

Choose Plots

If you use plots from MultiQC in a publication or presentation, please cite:

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

Settings are automatically saved. You can also save named configurations below.

Save Settings

You can save the toolbox settings for this report to the browser or as a file.

Load Settings

Choose a saved report profile from the browser or load from a file:

Tool Citations

Please remember to cite the tools that you use in your analysis.

To help with this, you can download publication details of the tools mentioned in this report:

About MultiQC

This report was generated using MultiQC, version 1.28

You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

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:

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.

JavaScript Disabled

MultiQC reports use JavaScript for plots and toolbox functions. It looks like you have JavaScript disabled in your web browser. Please note that many of the report functions will not work as intended.

Report generated on 2025-12-21, 21:21 UTC based on data in: /tmp/nxf.itzmpXxnEn

Sample Sheet

The sample sheet provided as input to the pipeline.

Showing ⁶/₆ rows and ⁵/₅ columns.

sample	file	type	response	data_directory
HC01BTC_visiumHD	samplesheet.csv	visium-hd	non-responder	s3://project-5678660b-483c-470c-a0b1-2476fb01fa56/datasets/e4b04bf1-f4e9-408f-9704-0d67d4e4e7cf/data
HC03BTC_visiumHD	samplesheet.csv	visium-hd	non-responder	s3://project-5678660b-483c-470c-a0b1-2476fb01fa56/datasets/2b620ce7-62ac-4c56-93d3-3910db3c7b15/data
HC04BTC_visiumHD	samplesheet.csv	visium-hd	non-responder	s3://project-5678660b-483c-470c-a0b1-2476fb01fa56/datasets/1fd5269a-5cc2-47aa-9363-867b02797acb/data
HC05BTC_visiumHD	samplesheet.csv	visium-hd	responder	s3://project-5678660b-483c-470c-a0b1-2476fb01fa56/datasets/f88669be-96e9-42f4-9fed-13bf1b734778/data
HC07BTC_visiumHD	samplesheet.csv	visium-hd	responder	s3://project-5678660b-483c-470c-a0b1-2476fb01fa56/datasets/7dc58554-509b-4abe-8d64-d515829ec8b2/data
HC08BTC_visiumHD	samplesheet.csv	visium-hd	responder	s3://project-5678660b-483c-470c-a0b1-2476fb01fa56/datasets/a3a9b3be-f793-4bcb-9c61-02f77dd52854/data

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
\|\|	file	file	`file`
\|\|	type	type	`type`
\|\|	response	response	`response`
\|\|	data_directory	data_directory	`data_directory`
\|\|	expression_profile	expression_profile	`expression_profile`

Atlas Summary

Summary of the cells and genes in the atlas. If same atlas is used for multiple samples, table rows will be repeated.

Showing ¹/₁ rows and ⁵/₅ columns.

Sample	n_genes	n_cells	mean_genes_by_counts	mean_cells_by_counts	mean_total_nnz_counts
lovelessAtlas_FULLreAnnot_PT	36601	562321	1300.9	19986.3	1.6

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`

Atlas Cell Types

Summary of the cell types in the atlas.

Showing ¹/₁ rows and ¹³/₁₃ columns.

Sample	PDAC	TNK	FIBROBLASTS	MYELOID	ENDOTHELIAL	PERICYTES	ENDOCRINE	CYCLING TNK	ACINAR	B CELLS	PLASMA	MAST	CYCLING. MYELOID
lovelessAtlas_FULLreAnnot_PT	227293	92517	61957	54465	31908	31487	15344	14011	13990	8941	5353	3070	1985

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
\|\|	PDAC	PDAC	`PDAC`
\|\|	TNK	TNK	`TNK`
\|\|	FIBROBLASTS	FIBROBLASTS	`FIBROBLASTS`
\|\|	MYELOID	MYELOID	`MYELOID`
\|\|	ENDOTHELIAL	ENDOTHELIAL	`ENDOTHELIAL`
\|\|	PERICYTES	PERICYTES	`PERICYTES`
\|\|	ENDOCRINE	ENDOCRINE	`ENDOCRINE`
\|\|	CYCLING TNK	CYCLING TNK	`CYCLING_TNK`
\|\|	ACINAR	ACINAR	`ACINAR`
\|\|	B CELLS	B CELLS	`B_CELLS`
\|\|	PLASMA	PLASMA	`PLASMA`
\|\|	MAST	MAST	`MAST`
\|\|	CYCLING. MYELOID	CYCLING. MYELOID	`CYCLING_MYELOID`

Input Summary

Summary of the AnnData object right after it was read.

Showing ⁶/₆ rows and ⁵/₅ columns.

Sample	n_genes	n_cells	mean_genes_by_counts	mean_cells_by_counts	mean_total_nnz_counts
HC01BTC_visiumHD	18085	169550	267.6	2508.9	1.2
HC03BTC_visiumHD	18085	175561	176.9	1717.5	1.3
HC04BTC_visiumHD	18085	163383	187.0	1689.7	1.2
HC05BTC_visiumHD	18085	164263	97.4	885.0	2.4
HC07BTC_visiumHD	18085	175561	82.6	802.3	1.2
HC08BTC_visiumHD	18085	142989	91.7	725.0	1.2

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`

Output Cell Types

Assigned cell types based on deconvolution / cell typing results.

Showing ⁶/₆ rows and ¹³/₁₃ columns.

Sample	FIBROBLASTS	PERICYTES	ENDOTHELIAL	MYELOID	TNK	PLASMA	CYCLING MYELOID	B CELLS	PDAC	MAST	CYCLING TNK	ENDOCRINE	ACINAR
HC01BTC_visiumHD	69598	1334	4897	5637	305	409	573	43	45773	136	24	982	184
HC03BTC_visiumHD	107940	2123	2251	929	42	219	280	173	22685	40		1743	331
HC04BTC_visiumHD	70488	1452	2333	9737	1580	2070	1419	149	18503	56	26	1762	382
HC05BTC_visiumHD	11007	1532	1809	263	615	41	256	131	12245	124	47	3922	37253
HC07BTC_visiumHD	38989	1390	732	4102	2036	400	395	554	3213	94	48	3923	193
HC08BTC_visiumHD	20757	18231	5704	3921	3722	1817	1212	1051	622	160	131	73	4

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
\|\|	FIBROBLASTS	FIBROBLASTS	`FIBROBLASTS`
\|\|	PERICYTES	PERICYTES	`PERICYTES`
\|\|	ENDOTHELIAL	ENDOTHELIAL	`ENDOTHELIAL`
\|\|	MYELOID	MYELOID	`MYELOID`
\|\|	TNK	TNK	`TNK`
\|\|	PLASMA	PLASMA	`PLASMA`
\|\|	CYCLING MYELOID	CYCLING MYELOID	`CYCLING_MYELOID`
\|\|	B CELLS	B CELLS	`B_CELLS`
\|\|	PDAC	PDAC	`PDAC`
\|\|	MAST	MAST	`MAST`
\|\|	CYCLING TNK	CYCLING TNK	`CYCLING_TNK`
\|\|	ENDOCRINE	ENDOCRINE	`ENDOCRINE`
\|\|	ACINAR	ACINAR	`ACINAR`

Cell Type Probabilities

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

Showing ⁶/₆ rows and ¹³/₁₃ columns.

Sample	ACINAR	B CELLS	CYCLING MYELOID	CYCLING TNK	ENDOCRINE	ENDOTHELIAL	FIBROBLASTS	MAST	MYELOID	PDAC	PERICYTES	PLASMA	TNK
HC01BTC_visiumHD	0.5	0.3	0.4	0.3	0.5	0.5	0.6	0.4	0.5	0.7	0.4	0.4	0.4
HC03BTC_visiumHD	0.4	0.5	0.4		0.6	0.5	0.7	0.3	0.4	0.6	0.4	0.5	0.4
HC04BTC_visiumHD	0.4	0.4	0.4	0.3	0.6	0.4	0.6	0.3	0.5	0.7	0.4	0.4	0.4
HC05BTC_visiumHD	0.8	0.3	0.3	0.3	0.7	0.4	0.5	0.3	0.4	0.6	0.4	0.4	0.4
HC07BTC_visiumHD	0.4	0.4	0.4	0.3	0.6	0.5	0.6	0.3	0.5	0.5	0.4	0.5	0.4
HC08BTC_visiumHD	0.8	0.4	0.4	0.4	0.4	0.5	0.6	0.4	0.4	0.6	0.9	0.5	0.4

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
\|\|	ACINAR	ACINAR	`ACINAR`
\|\|	B CELLS	B CELLS	`B_CELLS`
\|\|	CYCLING MYELOID	CYCLING MYELOID	`CYCLING_MYELOID`
\|\|	CYCLING TNK	CYCLING TNK	`CYCLING_TNK`
\|\|	ENDOCRINE	ENDOCRINE	`ENDOCRINE`
\|\|	ENDOTHELIAL	ENDOTHELIAL	`ENDOTHELIAL`
\|\|	FIBROBLASTS	FIBROBLASTS	`FIBROBLASTS`
\|\|	MAST	MAST	`MAST`
\|\|	MYELOID	MYELOID	`MYELOID`
\|\|	PDAC	PDAC	`PDAC`
\|\|	PERICYTES	PERICYTES	`PERICYTES`
\|\|	PLASMA	PLASMA	`PLASMA`
\|\|	TNK	TNK	`TNK`

Moran I Interactions

Mean interaction across samples shown as no differential interactions were found between ['HC03BTC_visiumHD', 'HC01BTC_visiumHD', 'HC04BTC_visiumHD'] and ['HC05BTC_visiumHD', 'HC08BTC_visiumHD', 'HC07BTC_visiumHD'].

Created with MultiQC

Spatial Neighbors

Cell type immediate neighborhood across samples.

Created with MultiQC

Spacemarkers Lrscores Interactions

Differential interactions between ['HC03BTC_visiumHD', 'HC01BTC_visiumHD', 'HC04BTC_visiumHD'] and ['HC05BTC_visiumHD', 'HC08BTC_visiumHD', 'HC07BTC_visiumHD']. Top 100 shown sorted by adjusted p-value between 2.34e-02 and 4.81e-02.

Created with MultiQC

Software Versions

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

Group	Software	Version
ADATA_ADD_METADATA	anndata	`0.12.6`
ADATA_FROM_VISIUM_HD	spatialdata_io	`0.5.1`
	squidpy	`1.6.6.dev24+g32789aefd`
ATLAS_GET	boto3	`1.41.2`
	requests	`2.32.5`
ATLAS_MATCH	anndata	`0.12.6`
	numpy	`2.3.5`
QC	anndata	`0.12.6`
	pandas	`2.3.3`
RCTD	Matrix	`1.7-4`
	R	`4.5.2`
	reticulate	`1.44.1`
	spacexr	`2.2.1`
SQUIDPY_SPATIAL_PLOTS	anndata	`0.12.6`
	numpy	`2.3.5`
	python	`3.11.14`
	squidpy	`1.6.6.dev24+g32789aefd`
STAPLE_XSAMPLE	anndata	`0.12.6`
	json	`2.0.9`
	numpy	`2.3.5`
	pandas	`2.3.3`
	scipy	`1.16.3`
Workflow	Nextflow	`25.04.8`
	STAPLE	`v2.0.0-gb5f784d`
process	Biobase	`2.70.0`
	BiocGenerics	`0.56.0`
	CellChat	`2.2.0`
	R	`4.5.2`
	SpaceMarkers	`2.1.0`
	dplyr	`1.1.4`
	effsize	`0.8.1`
	generics	`0.1.4`
	ggplot2	`4.0.0`
	igraph	`2.2.1`

Toggle navigation v1.28

MultiQC Toolbox

Apply Highlight Samples

Apply Rename Samples

Apply Show / Hide Samples

Explain with AI

Export Plots

Choose Plots

Save Settings

Load Settings

Tool Citations

About MultiQC

Sample Sheet

Sample Sheet: Columns

Atlas Summary

Atlas Summary: Columns

Atlas Cell Types

Atlas Cell Types: Columns

Input Summary

Input Summary: Columns

Output Cell Types

Output Cell Types: Columns

Cell Type Probabilities

Cell Type Probabilities: Columns

Moran I Interactions

Spatial Neighbors

Spacemarkers Lrscores Interactions

Software Versions

v1.28

Highlight Samples

Rename Samples

Show / Hide Samples