MultiQC Report

Sample Sheet

The sample sheet provided as input to the pipeline. Sample sheet contains sample name, paths to the input data files and associated metadata.

Showing ⁶/₆ rows and ⁹/₉ columns.

sample	data_directory	patient	year_born	gender	timepoint	timepoint_date	sample_type	radiotherapy
T0-0078011	/local/projects-t3/fertig_staple/osteosarc/xenium/T0/output-XETG00279__0078011__B3__20260211__182948	XETG00279	1979	male	T0	2022-11	resection	pre
T0-0078018	/local/projects-t3/fertig_staple/osteosarc/xenium/T0/output-XETG00279__0078018__C3__20260211__182947	XETG00279	1979	male	T0	2022-11	resection	pre
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	pre
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	pre
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	post
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	post

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`
\|\|	radiotherapy	radiotherapy	`radiotherapy`

Input Data

Summaries of the input datasets.

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-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`

Reference Cell Types

Summary of the cell types in the atlas. Provides an overview of the diversity and abundance of cell types used as reference in deconvolution.

Showing ¹/₁ rows and ¹⁶/₁₆ columns.

Sample	T_Cells_CD8	T_Cells_CD4	Macrophages	Tumor	Mito	Endothelial_cells	B_cells	Monocytes_classical	Neutrophils	NK_cells	Ribo	Osteoclasts	Macrophages_perivascular	cDCs	Monocytes_non_classical	pDCs
072925_IPISRC044_T1_T2_T3_sobj_merged_processed_tcr_bcr_mutMap_tcMap_annot_final_reannot	9426	4343	4198	3571	1391	975	830	728	636	583	442	419	211	136	107	50

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

Sort	Column	Description	ID
\|\|	T_Cells_CD8	T_Cells_CD8	`T_Cells_CD8`
\|\|	T_Cells_CD4	T_Cells_CD4	`T_Cells_CD4`
\|\|	Macrophages	Macrophages	`Macrophages`
\|\|	Tumor	Tumor	`Tumor`
\|\|	Mito	Mito	`Mito`
\|\|	Endothelial_cells	Endothelial_cells	`Endothelial_cells`
\|\|	B_cells	B_cells	`B_cells`
\|\|	Monocytes_classical	Monocytes_classical	`Monocytes_classical`
\|\|	Neutrophils	Neutrophils	`Neutrophils`
\|\|	NK_cells	NK_cells	`NK_cells`
\|\|	Ribo	Ribo	`Ribo`
\|\|	Osteoclasts	Osteoclasts	`Osteoclasts`
\|\|	Macrophages_perivascular	Macrophages_perivascular	`Macrophages_perivascular`
\|\|	cDCs	cDCs	`cDCs`
\|\|	Monocytes_non_classical	Monocytes_non_classical	`Monocytes_non_classical`
\|\|	pDCs	pDCs	`pDCs`

Reference Summary

Summary of the cells and genes in the atlas. Atlas is used as a reference for deconvolution and cell type assignment.

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_reannot	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-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`

Cell Typing

Summaries of the cell typing results.

Cell Type Counts

Assigned cell types based on deconvolution / cell typing results. Unassigned counts appear in a column with no header.

Showing ⁶/₆ rows and ¹⁷/₁₇ columns.

Sample	Tumor		Endothelial cells	Macrophages	T Cells CD8	B cells	Osteoclasts	T Cells CD4	Monocytes classical	Macrophages perivascular	Mito	cDCs	Ribo	pDCs	NK cells	Monocytes non classical	Neutrophils
T0-0078011	164735	105697	25594	9468	2567	1771	1395	1291	1143	1022	899	702	520	503	487	391	135
T0-0078018	294379	79307	23437	14141	1283	182	702	1159	743	7129	1956	657	939	60	259	99	94
T1-0102917	25179	4545	1721	719	203	15	113	93	817	591	53	165	80	8	80	75	21
T2-0102913	66927	22905	2995	10319	6108	2911	695	2168	1596	899	838	2424	529	117	585	175	11
T3-0103076	63304	164294	1779	16936	9889	1148	2851	4837	1990	1394	1387	1132	1037	153	844	155	26
T3-0103350	61252	104549	1283	13729	7610	620	2263	3646	1545	1014	1379	839	852	98	638	163	23

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

Sort	Column	Description	ID
\|\|	Tumor	Tumor	`Tumor`
\|\|			`mqc_`
\|\|	Endothelial cells	Endothelial cells	`Endothelial_cells`
\|\|	Macrophages	Macrophages	`Macrophages`
\|\|	T Cells CD8	T Cells CD8	`T_Cells_CD8`
\|\|	B cells	B cells	`B_cells`
\|\|	Osteoclasts	Osteoclasts	`Osteoclasts`
\|\|	T Cells CD4	T Cells CD4	`T_Cells_CD4`
\|\|	Monocytes classical	Monocytes classical	`Monocytes_classical`
\|\|	Macrophages perivascular	Macrophages perivascular	`Macrophages_perivascular`
\|\|	Mito	Mito	`Mito`
\|\|	cDCs	cDCs	`cDCs`
\|\|	Ribo	Ribo	`Ribo`
\|\|	pDCs	pDCs	`pDCs`
\|\|	NK cells	NK cells	`NK_cells`
\|\|	Monocytes non classical	Monocytes non classical	`Monocytes_non_classical`
\|\|	Neutrophils	Neutrophils	`Neutrophils`

Cell Type Probabilities

Average max cell type probabilities (fractions) used to assign the cell types. Greater values indicate more homogenous cell type assignments.

Showing ⁶/₆ rows and ¹⁶/₁₆ columns.

Sample	B cells	Endothelial cells	Macrophages	Macrophages perivascular	Mito	Monocytes classical	Monocytes non classical	NK cells	Neutrophils	Osteoclasts	Ribo	T Cells CD4	T Cells CD8	Tumor	cDCs	pDCs
T0-0078011	0.5	0.7	0.5	0.4	0.4	0.5	0.4	0.5	0.4	0.6	0.5	0.6	0.5	0.8	0.5	0.4
T0-0078018	0.3	0.6	0.4	0.4	0.4	0.4	0.4	0.5	0.6	0.4	0.5	0.5	0.5	0.8	0.4	0.3
T1-0102917	0.3	0.7	0.5	0.4	0.4	0.5	0.5	0.6	0.5	0.4	0.5	0.6	0.6	0.8	0.4	0.3
T2-0102913	0.5	0.7	0.5	0.4	0.4	0.5	0.4	0.4	0.3	0.4	0.4	0.5	0.5	0.8	0.5	0.5
T3-0103076	0.5	0.7	0.6	0.5	0.5	0.5	0.6	0.5	0.4	0.5	0.4	0.5	0.6	0.8	0.6	0.6
T3-0103350	0.5	0.7	0.6	0.5	0.5	0.5	0.5	0.5	0.3	0.5	0.4	0.5	0.5	0.8	0.6	0.6

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

Sort	Column	Description	ID
\|\|	B cells	B cells	`B_cells`
\|\|	Endothelial cells	Endothelial cells	`Endothelial_cells`
\|\|	Macrophages	Macrophages	`Macrophages`
\|\|	Macrophages perivascular	Macrophages perivascular	`Macrophages_perivascular`
\|\|	Mito	Mito	`Mito`
\|\|	Monocytes classical	Monocytes classical	`Monocytes_classical`
\|\|	Monocytes non classical	Monocytes non classical	`Monocytes_non_classical`
\|\|	NK cells	NK cells	`NK_cells`
\|\|	Neutrophils	Neutrophils	`Neutrophils`
\|\|	Osteoclasts	Osteoclasts	`Osteoclasts`
\|\|	Ribo	Ribo	`Ribo`
\|\|	T Cells CD4	T Cells CD4	`T_Cells_CD4`
\|\|	T Cells CD8	T Cells CD8	`T_Cells_CD8`
\|\|	Tumor	Tumor	`Tumor`
\|\|	cDCs	cDCs	`cDCs`
\|\|	pDCs	pDCs	`pDCs`

Graph Stats

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

Average Clustering

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

Showing ⁶/₆ rows and ¹⁷/₁₇ columns.

Sample Name	B cells	Endothelial cells	Macrophages	Macrophages perivascular	Mito	Monocytes classical	Monocytes non classical	NK cells	Neutrophils	Osteoclasts	Ribo	T Cells CD4	T Cells CD8	Tumor	cDCs	pDCs	NA
T0-0078011	0.4	0.5	0.4	0.4	0.5	0.4	0.3	0.5	0.4	0.4	0.5	0.5	0.5	0.4	0.5	0.4	0.4
T0-0078018	0.5	0.5	0.5	0.5	0.5	0.5	0.5	0.5	0.4	0.5	0.5	0.5	0.5	0.4	0.5	0.5	0.5
T1-0102917	0.3	0.4	0.4	0.4	0.5	0.3	0.4	0.3	0.3	0.3	0.4	0.4	0.4	0.4	0.4	0.5	0.4
T2-0102913	0.4	0.4	0.4	0.4	0.4	0.4	0.5	0.4	0.4	0.5	0.4	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	0.3	0.4	0.3	0.4	0.4	0.4	0.4	0.4	0.4	0.4	0.3
T3-0103350	0.4	0.4	0.4	0.4	0.4	0.4	0.3	0.4	0.4	0.4	0.4	0.4	0.4	0.4	0.4	0.4	0.3

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

Sort	Column	Description	ID
\|\|	B cells	B cells	`B_cells`
\|\|	Endothelial cells	Endothelial cells	`Endothelial_cells`
\|\|	Macrophages	Macrophages	`Macrophages`
\|\|	Macrophages perivascular	Macrophages perivascular	`Macrophages_perivascular`
\|\|	Mito	Mito	`Mito`
\|\|	Monocytes classical	Monocytes classical	`Monocytes_classical`
\|\|	Monocytes non classical	Monocytes non classical	`Monocytes_non_classical`
\|\|	NK cells	NK cells	`NK_cells`
\|\|	Neutrophils	Neutrophils	`Neutrophils`
\|\|	Osteoclasts	Osteoclasts	`Osteoclasts`
\|\|	Ribo	Ribo	`Ribo`
\|\|	T Cells CD4	T Cells CD4	`T_Cells_CD4`
\|\|	T Cells CD8	T Cells CD8	`T_Cells_CD8`
\|\|	Tumor	Tumor	`Tumor`
\|\|	cDCs	cDCs	`cDCs`
\|\|	pDCs	pDCs	`pDCs`
\|\|	NA	NA	`NA`

Closeness Centrality

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

Showing ⁶/₆ rows and ¹⁷/₁₇ columns.

Sample Name	B cells	Endothelial cells	Macrophages	Macrophages perivascular	Mito	Monocytes classical	Monocytes non classical	NK cells	Neutrophils	Osteoclasts	Ribo	T Cells CD4	T Cells CD8	Tumor	cDCs	pDCs	NA
T0-0078011	0.0	0.4	0.3	0.1	0.1	0.1	0.0	0.1	0.0	0.1	0.1	0.1	0.1	0.6	0.1	0.0	0.4
T0-0078018	0.0	0.3	0.3	0.2	0.1	0.1	0.0	0.0	0.0	0.0	0.1	0.1	0.1	0.8	0.1	0.0	0.3
T1-0102917	0.0	0.4	0.2	0.2	0.1	0.2	0.0	0.1	0.4	0.1	0.1	0.1	0.1	1.4	0.1	0.0	0.2
T2-0102913	0.1	0.2	0.3	0.1	0.1	0.1	0.0	0.1	0.0	0.1	0.1	0.2	0.3	0.3	0.2	0.0	0.3
T3-0103076	0.2	0.3	0.5	0.2	0.2	0.2	0.1	0.3	0.1	0.3	0.3	0.5	0.4	0.4	0.2	0.1	0.5
T3-0103350	0.2	0.2	0.5	0.2	0.2	0.2	0.1	0.2	0.0	0.3	0.2	0.3	0.5	0.7	0.2	0.1	0.4

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

Sort	Column	Description	ID
\|\|	B cells	B cells	`B_cells`
\|\|	Endothelial cells	Endothelial cells	`Endothelial_cells`
\|\|	Macrophages	Macrophages	`Macrophages`
\|\|	Macrophages perivascular	Macrophages perivascular	`Macrophages_perivascular`
\|\|	Mito	Mito	`Mito`
\|\|	Monocytes classical	Monocytes classical	`Monocytes_classical`
\|\|	Monocytes non classical	Monocytes non classical	`Monocytes_non_classical`
\|\|	NK cells	NK cells	`NK_cells`
\|\|	Neutrophils	Neutrophils	`Neutrophils`
\|\|	Osteoclasts	Osteoclasts	`Osteoclasts`
\|\|	Ribo	Ribo	`Ribo`
\|\|	T Cells CD4	T Cells CD4	`T_Cells_CD4`
\|\|	T Cells CD8	T Cells CD8	`T_Cells_CD8`
\|\|	Tumor	Tumor	`Tumor`
\|\|	cDCs	cDCs	`cDCs`
\|\|	pDCs	pDCs	`pDCs`
\|\|	NA	NA	`NA`

Degree Centrality

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

Showing ⁶/₆ rows and ¹⁷/₁₇ columns.

Sample Name	B cells	Endothelial cells	Macrophages	Macrophages perivascular	Monocytes classical	Osteoclasts	T Cells CD4	T Cells CD8	Tumor	cDCs	NA
T0-0078011	0.0	0.2	0.1	0.0	0.0	0.0	0.0	0.0	0.4	0.0	0.3
T0-0078018	0.0	0.2	0.1	0.1	0.0	0.0	0.0	0.0	0.7	0.0	0.2
T1-0102917	0.0	0.2	0.1	0.1	0.1	0.0	0.0	0.0	0.5	0.0	0.1
T2-0102913	0.1	0.1	0.2	0.0	0.1	0.0	0.1	0.2	0.4	0.1	0.2
T3-0103076	0.0	0.0	0.2	0.0	0.0	0.1	0.1	0.2	0.2	0.0	0.5
T3-0103350	0.0	0.0	0.2	0.0	0.0	0.1	0.1	0.2	0.3	0.0	0.4

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

Sort	Column	Description	ID
\|\|	B cells	B cells	`B_cells`
\|\|	Endothelial cells	Endothelial cells	`Endothelial_cells`
\|\|	Macrophages	Macrophages	`Macrophages`
\|\|	Macrophages perivascular	Macrophages perivascular	`Macrophages_perivascular`
\|\|	Mito	Mito	`Mito`
\|\|	Monocytes classical	Monocytes classical	`Monocytes_classical`
\|\|	Monocytes non classical	Monocytes non classical	`Monocytes_non_classical`
\|\|	NK cells	NK cells	`NK_cells`
\|\|	Neutrophils	Neutrophils	`Neutrophils`
\|\|	Osteoclasts	Osteoclasts	`Osteoclasts`
\|\|	Ribo	Ribo	`Ribo`
\|\|	T Cells CD4	T Cells CD4	`T_Cells_CD4`
\|\|	T Cells CD8	T Cells CD8	`T_Cells_CD8`
\|\|	Tumor	Tumor	`Tumor`
\|\|	cDCs	cDCs	`cDCs`
\|\|	pDCs	pDCs	`pDCs`
\|\|	NA	NA	`NA`

Spatial Neighbors

Cell type 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. Self is omitted in this report based on the pipeline settings.

Created with MultiQC

Moran I By Radiotherapy

Top 50 differential scores across samples. There are 20 significant differential scores (p_adj<=0.05) found between ['T3-0103350', 'T3-0103076'] and ['T1-0102917', 'T2-0102913', 'T0-0078011', 'T0-0078018'], marked with *.

Created with MultiQC

Co Occurrence By Radiotherapy

Median difference of co-occurrence across groups by variable radiotherapy (post - pre). The plot is organized by focal cell type and displays differences in co-occurrence of each other cell type with the focal cell type at each of the observed intervals. Spotlight mode on ['Tumor'].

Created with MultiQC

Deseq2 By Radiotherapy

DESeq2 results for radiotherapy variable with significant DE genes (padj<=0.05) between post and pre. Log2 fold change (X) and -log10 adjusted p-value (Y) shown.

Created with MultiQC

Neighbors By Radiotherapy

Neighbors By Radiotherapy cell_type-neighbors by radiotherapy: t-test on ALR normalized counts relative to self-neighbors. Spotlight on ['Tumor']. There are 0 significant (p_adj<=0.05) results marked with *.

Showing ⁶/₆ rows and ¹⁶/₁₆ columns.

Sample Name	Tumor-Osteoclasts	Tumor-Endothelial cells	Tumor-NK cells	Tumor-Macrophages	Tumor-T Cells CD4	Tumor-T Cells CD8	Tumor-Ribo	Tumor-Mito	Tumor-NA	Tumor-B cells	Tumor-Neutrophils	Tumor-Monocytes classical	Tumor-cDCs	Tumor-Monocytes non classical	Tumor-pDCs	Tumor-Macrophages perivascular
T0-0078011	-5.2	-2.5	-7.0	-3.1	-6.1	-5.5	-6.8	-5.7	-2.4	-6.9	-8.8	-6.6	-6.3	-8.4	-7.5	-6.3
T0-0078018	-6.1	-2.7	-7.2	-3.1	-5.6	-5.6	-5.8	-5.0	-2.5	-7.6	-9.1	-6.1	-6.3	-8.5	-8.7	-3.8
T1-0102917	-6.0	-2.8	-6.5	-3.9	-6.0	-5.0	-6.0	-6.2	-3.7	-7.8	-10.9	-4.2	-5.4	-7.3	-8.3	-3.9
T2-0102913	-6.1	-3.8	-6.3	-3.0	-4.5	-3.7	-5.8	-5.0	-3.3	-4.8	-11.0	-4.6	-4.3	-7.7	-7.9	-6.1
T3-0103076	-3.7	-4.4	-5.2	-1.9	-3.3	-2.5	-4.8	-4.3	-1.7	-4.9	-8.8	-4.5	-5.0	-7.5	-7.4	-4.5
T3-0103350	-3.9	-4.6	-5.3	-2.0	-3.4	-2.6	-4.9	-4.3	-1.9	-5.4	-8.7	-4.6	-5.1	-7.7	-8.1	-4.8

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

Sort	Column	Description	ID
\|\|	Tumor-Osteoclasts	Tumor-Osteoclasts	`Tumor_Osteoclasts`
\|\|	Tumor-Endothelial cells	Tumor-Endothelial cells	`Tumor_Endothelial_cells`
\|\|	Tumor-NK cells	Tumor-NK cells	`Tumor_NK_cells`
\|\|	Tumor-Macrophages	Tumor-Macrophages	`Tumor_Macrophages`
\|\|	Tumor-T Cells CD4	Tumor-T Cells CD4	`Tumor_T_Cells_CD4`
\|\|	Tumor-T Cells CD8	Tumor-T Cells CD8	`Tumor_T_Cells_CD8`
\|\|	Tumor-Ribo	Tumor-Ribo	`Tumor_Ribo`
\|\|	Tumor-Mito	Tumor-Mito	`Tumor_Mito`
\|\|	Tumor-NA	Tumor-NA	`Tumor_NA`
\|\|	Tumor-B cells	Tumor-B cells	`Tumor_B_cells`
\|\|	Tumor-Neutrophils	Tumor-Neutrophils	`Tumor_Neutrophils`
\|\|	Tumor-Monocytes classical	Tumor-Monocytes classical	`Tumor_Monocytes_classical`
\|\|	Tumor-cDCs	Tumor-cDCs	`Tumor_cDCs`
\|\|	Tumor-Monocytes non classical	Tumor-Monocytes non classical	`Tumor_Monocytes_non_classical`
\|\|	Tumor-pDCs	Tumor-pDCs	`Tumor_pDCs`
\|\|	Tumor-Macrophages perivascular	Tumor-Macrophages perivascular	`Tumor_Macrophages_perivascular`

Squidpy Ligrec By Radiotherapy

Top 50 differential scores across samples. There are 4 significant differential scores (p_adj<=0.05) found between ['T3-0103350', 'T3-0103076'] and ['T1-0102917', 'T2-0102913', 'T0-0078011', 'T0-0078018'], marked with *.

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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`
ADATA_PREPROCESS	anndata	`0.12.11`
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	anndata	`0.12.10`
	numpy	`2.4.3`
	python	`3.11.15`
	squidpy	`1.6.6.dev24+g32789aefd`
STAPLE_XSAMPLE	anndata	`0.12.10`
	matplotlib	`3.10.8`
	numpy	`2.4.3`
	pandas	`2.3.3`
	pydeseq2	`0.5.4`
	scipy	`1.17.1`
	seaborn	`0.13.2`
Workflow	Nextflow	`26.04.1`
	STAPLE	`v2.5.0-g8ae233d`

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