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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

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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:

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 2026-02-06, 18:29 EST based on data in: /usr/local/scratch/dlvovs/work/98/29c02d487b3e7e5e960758935d9500

Sample Sheet

The sample sheet provided as input to the pipeline.

Showing ³⁸/₃₈ rows and ⁷/₇ columns.

sample	data_directory	brain	tissue	region	subject_status	age
GSM9227428	data/GSE307586/samples/GSM9227428	Br2720	nucleus accumbens	A1	neurotypical control postmortem human brain donor	48.2
GSM9227429	data/GSE307586/samples/GSM9227429	Br2720	nucleus accumbens	B1	neurotypical control postmortem human brain donor	48.2
GSM9227430	data/GSE307586/samples/GSM9227430	Br2720	nucleus accumbens	C1	neurotypical control postmortem human brain donor	48.2
GSM9227431	data/GSE307586/samples/GSM9227431	Br2720	nucleus accumbens	D1	neurotypical control postmortem human brain donor	48.2
GSM9227432	data/GSE307586/samples/GSM9227432	Br8492	nucleus accumbens	A1	neurotypical control postmortem human brain donor	53.4
GSM9227433	data/GSE307586/samples/GSM9227433	Br8492	nucleus accumbens	B1	neurotypical control postmortem human brain donor	53.4
GSM9227434	data/GSE307586/samples/GSM9227434	Br8492	nucleus accumbens	C1	neurotypical control postmortem human brain donor	53.4
GSM9227435	data/GSE307586/samples/GSM9227435	Br8492	nucleus accumbens	D1	neurotypical control postmortem human brain donor	53.4
GSM9227436	data/GSE307586/samples/GSM9227436	Br6522	nucleus accumbens	A1	neurotypical control postmortem human brain donor	33.4
GSM9227437	data/GSE307586/samples/GSM9227437	Br6522	nucleus accumbens	B1	neurotypical control postmortem human brain donor	33.4
GSM9227438	data/GSE307586/samples/GSM9227438	Br6522	nucleus accumbens	C1	neurotypical control postmortem human brain donor	33.4
GSM9227439	data/GSE307586/samples/GSM9227439	Br6522	nucleus accumbens	D1	neurotypical control postmortem human brain donor	33.4
GSM9227440	data/GSE307586/samples/GSM9227440	Br6423	nucleus accumbens	A1	neurotypical control postmortem human brain donor	51.7
GSM9227441	data/GSE307586/samples/GSM9227441	Br6423	nucleus accumbens	B1	neurotypical control postmortem human brain donor	51.7
GSM9227442	data/GSE307586/samples/GSM9227442	Br8325	nucleus accumbens	C1	neurotypical control postmortem human brain donor	57.6
GSM9227443	data/GSE307586/samples/GSM9227443	Br6423	nucleus accumbens	D1	neurotypical control postmortem human brain donor	51.7
GSM9227444	data/GSE307586/samples/GSM9227444	Br8325	nucleus accumbens	A1	neurotypical control postmortem human brain donor	57.6
GSM9227445	data/GSE307586/samples/GSM9227445	Br8325	nucleus accumbens	B1	neurotypical control postmortem human brain donor	57.6
GSM9227446	data/GSE307586/samples/GSM9227446	Br8325	nucleus accumbens	C1	neurotypical control postmortem human brain donor	57.6
GSM9227447	data/GSE307586/samples/GSM9227447	Br8325	nucleus accumbens	D1	neurotypical control postmortem human brain donor	57.6
GSM9227448	data/GSE307586/samples/GSM9227448	Br6432	nucleus accumbens	A1	neurotypical control postmortem human brain donor	48.9
GSM9227449	data/GSE307586/samples/GSM9227449	Br6432	nucleus accumbens	B1	neurotypical control postmortem human brain donor	48.9
GSM9227450	data/GSE307586/samples/GSM9227450	Br6432	nucleus accumbens	C1	neurotypical control postmortem human brain donor	48.9
GSM9227451	data/GSE307586/samples/GSM9227451	Br6432	nucleus accumbens	D1	neurotypical control postmortem human brain donor	48.9
GSM9227452	data/GSE307586/samples/GSM9227452	Br6471	nucleus accumbens	A1	neurotypical control postmortem human brain donor	55.5
GSM9227453	data/GSE307586/samples/GSM9227453	Br6471	nucleus accumbens	B1	neurotypical control postmortem human brain donor	55.5
GSM9227454	data/GSE307586/samples/GSM9227454	Br6471	nucleus accumbens	C1	neurotypical control postmortem human brain donor	55.5
GSM9227455	data/GSE307586/samples/GSM9227455	Br6471	nucleus accumbens	D1	neurotypical control postmortem human brain donor	55.5
GSM9227456	data/GSE307586/samples/GSM9227456	Br2743	nucleus accumbens	A1	neurotypical control postmortem human brain donor	61.5
GSM9227457	data/GSE307586/samples/GSM9227457	Br2743	nucleus accumbens	B1	neurotypical control postmortem human brain donor	61.5
GSM9227458	data/GSE307586/samples/GSM9227458	Br2743	nucleus accumbens	C1	neurotypical control postmortem human brain donor	61.5
GSM9227459	data/GSE307586/samples/GSM9227459	Br2743	nucleus accumbens	D1	neurotypical control postmortem human brain donor	61.5
GSM9227460	data/GSE307586/samples/GSM9227460	Br3942	nucleus accumbens	A1	neurotypical control postmortem human brain donor	47.5
GSM9227461	data/GSE307586/samples/GSM9227461	Br3942	nucleus accumbens	B1	neurotypical control postmortem human brain donor	47.5
GSM9227462	data/GSE307586/samples/GSM9227462	Br3942	nucleus accumbens	C1	neurotypical control postmortem human brain donor	47.5
GSM9227463	data/GSE307586/samples/GSM9227463	Br3942	nucleus accumbens	D1	neurotypical control postmortem human brain donor	47.5
GSM9227464	data/GSE307586/samples/GSM9227464	Br8667	nucleus accumbens	B1	neurotypical control postmortem human brain donor	37.3
GSM9227465	data/GSE307586/samples/GSM9227465	Br8667	nucleus accumbens	C1	neurotypical control postmortem human brain donor	37.3

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`
\|\|	brain	brain	`brain`
\|\|	tissue	tissue	`tissue`
\|\|	region	region	`region`
\|\|	subject_status	subject_status	`subject_status`
\|\|	age	age	`age`

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
Human_HMBA_basalganglia_AIT_pre-print_NAC	36601	116884	5239.4	16731.9	4.5

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 ³³/₃₃ columns.

Sample	STR D1 MSN	STR D2 MSN	Astrocyte	Oligodendrocyte	STR Hybrid MSN	CN ST18 GABA	Microglia	OPC	Ependymal	STR RSPO2 GABA	CN VIP GABA	OT Granular GABA	STR SST-CHODL GABA	Endo	VLMC	ACx MEIS2 GABA	Pericyte	CN LAMP5-CXCL14 GABA	Macrophage	CN LAMP5-LHX6 GABA	F GABA	Lymphocyte	COP	CN Cholinergic GABA	SMC	CN LHX8 GABA	CN MEIS2 GABA	Monocyte	F M GATA3 GABA	STR SST GABA	F Glut	F M Glut	SN PAX7 GABA
Human_HMBA_basalganglia_AIT_pre-print_NAC	32743	32219	14136	9901	8528	5338	5061	2455	1689	884	636	474	421	361	322	319	251	250	198	190	115	109	67	64	59	39	22	14	6	4	4	3	2

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
\|\|	STR D1 MSN	STR D1 MSN	`STR_D1_MSN`
\|\|	STR D2 MSN	STR D2 MSN	`STR_D2_MSN`
\|\|	Astrocyte	Astrocyte	`Astrocyte`
\|\|	Oligodendrocyte	Oligodendrocyte	`Oligodendrocyte`
\|\|	STR Hybrid MSN	STR Hybrid MSN	`STR_Hybrid_MSN`
\|\|	CN ST18 GABA	CN ST18 GABA	`CN_ST18_GABA`
\|\|	Microglia	Microglia	`Microglia`
\|\|	OPC	OPC	`OPC`
\|\|	Ependymal	Ependymal	`Ependymal`
\|\|	STR RSPO2 GABA	STR RSPO2 GABA	`STR_RSPO2_GABA`
\|\|	CN VIP GABA	CN VIP GABA	`CN_VIP_GABA`
\|\|	OT Granular GABA	OT Granular GABA	`OT_Granular_GABA`
\|\|	STR SST-CHODL GABA	STR SST-CHODL GABA	`STR_SST_CHODL_GABA`
\|\|	Endo	Endo	`Endo`
\|\|	VLMC	VLMC	`VLMC`
\|\|	ACx MEIS2 GABA	ACx MEIS2 GABA	`ACx_MEIS2_GABA`
\|\|	Pericyte	Pericyte	`Pericyte`
\|\|	CN LAMP5-CXCL14 GABA	CN LAMP5-CXCL14 GABA	`CN_LAMP5_CXCL14_GABA`
\|\|	Macrophage	Macrophage	`Macrophage`
\|\|	CN LAMP5-LHX6 GABA	CN LAMP5-LHX6 GABA	`CN_LAMP5_LHX6_GABA`
\|\|	F GABA	F GABA	`F_GABA`
\|\|	Lymphocyte	Lymphocyte	`Lymphocyte`
\|\|	COP	COP	`COP`
\|\|	CN Cholinergic GABA	CN Cholinergic GABA	`CN_Cholinergic_GABA`
\|\|	SMC	SMC	`SMC`
\|\|	CN LHX8 GABA	CN LHX8 GABA	`CN_LHX8_GABA`
\|\|	CN MEIS2 GABA	CN MEIS2 GABA	`CN_MEIS2_GABA`
\|\|	Monocyte	Monocyte	`Monocyte`
\|\|	F M GATA3 GABA	F M GATA3 GABA	`F_M_GATA3_GABA`
\|\|	STR SST GABA	STR SST GABA	`STR_SST_GABA`
\|\|	F Glut	F Glut	`F_Glut`
\|\|	F M Glut	F M Glut	`F_M_Glut`
\|\|	SN PAX7 GABA	SN PAX7 GABA	`SN_PAX7_GABA`

Input Summary

Summary of the AnnData object right after it was read.

Showing ³⁸/₃₈ rows and ⁵/₅ columns.

Sample	n_genes	n_cells	mean_genes_by_counts	mean_cells_by_counts	mean_total_nnz_counts
GSM9227428	36601	4992	1659.9	226.4	2.0
GSM9227429	36601	4992	2652.0	361.7	2.3
GSM9227430	36601	4992	2590.1	353.3	2.2
GSM9227431	36601	4992	2616.5	356.9	2.2
GSM9227432	36601	4991	1583.6	215.9	2.0
GSM9227433	36601	4992	1481.7	202.1	2.0
GSM9227434	36601	4992	1555.5	212.2	2.1
GSM9227435	36601	4992	1671.5	228.0	2.0
GSM9227436	36601	4992	2654.3	362.0	2.6
GSM9227437	36601	4992	2615.9	356.8	2.5
GSM9227438	36601	4992	2710.2	369.6	2.3
GSM9227439	36601	4992	2262.6	308.6	2.3
GSM9227440	36601	4992	1682.1	229.4	1.8
GSM9227441	36601	4992	1094.1	149.2	1.8
GSM9227442	36601	4992	2569.1	350.4	2.1
GSM9227443	36601	4992	2152.4	293.6	2.0
GSM9227444	36601	4992	2393.1	326.4	2.2
GSM9227445	36601	4992	2271.3	309.8	2.1
GSM9227446	36601	4992	2171.0	296.1	2.1
GSM9227447	36601	4992	2409.4	328.6	2.1
GSM9227448	36601	4992	2125.8	289.9	2.1
GSM9227449	36601	4992	1405.6	191.7	1.9
GSM9227450	36601	4992	875.2	119.4	1.6
GSM9227451	36601	4992	1825.0	248.9	2.0
GSM9227452	36601	4992	2023.6	276.0	1.9
GSM9227453	36601	4992	2160.2	294.6	1.8
GSM9227454	36601	4992	1634.5	222.9	1.7
GSM9227455	36601	4992	1797.2	245.1	1.8
GSM9227456	36601	4992	1688.3	230.3	2.0
GSM9227457	36601	4992	1463.8	199.6	1.9
GSM9227458	36601	4992	1067.2	145.5	2.0
GSM9227459	36601	4992	949.5	129.5	1.9
GSM9227460	36601	4992	2131.7	290.7	2.2
GSM9227461	36601	4992	1699.6	231.8	2.2
GSM9227462	36601	4992	1586.8	216.4	2.1
GSM9227463	36601	4992	1829.1	249.5	2.1
GSM9227464	36601	4974	2628.0	357.1	2.5
GSM9227465	36601	4976	2037.3	277.0	2.4

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 ³⁸/₃₈ rows and ²⁶/₂₆ columns.

Sample	STR D2 MSN	Astrocyte	STR D1 MSN	CN ST18 GABA	Oligodendrocyte	STR Hybrid MSN	CN Cholinergic GABA	STR SST CHODL GABA	Endo	Pericyte	F GABA	CN LHX8 GABA	STR RSPO2 GABA	OT Granular GABA	SMC	ACx MEIS2 GABA	OPC	CN LAMP5 CXCL14 GABA	Lymphocyte	CN LAMP5 LHX6 GABA	CN VIP GABA	VLMC	Microglia	Ependymal	COP	Macrophage
GSM9227428	696	1663	649	334	565	245	156	48	103	85	33	123	13	83	32	121	9		11	6	1	4	4	5	1	1
GSM9227429	1963	817	1231	125	602	50	71	39	31	20	20	2	5	7		1			4	2		1			1
GSM9227430	808	1136	1642	170	921	59	37	41	32	12	19	19	1	64	1	2	1					1		25
GSM9227431	868	1343	808	649	552	120	134	51	33	25	77	108	14	142	1	47	5	1	5	4	1
GSM9227432	1967	188	1201	152	742	218	110	36	33	47	28	29	14	18	8	21	8	2	20	1	4	7	1	2	10	2
GSM9227433	2072	129	1082	87	1154	74	42	30	23	77	21	7	12	17	5	8	7	3	12	1		8	1	2	2	1
GSM9227434	1910	57	1248	123	560	515	82	41	18	51	29	30	11	28	4	16	5	1	33	6	1	7	3	6	3	3
GSM9227435	2523	71	946	122	909	140	55	23	42	49	15	5	14	14	9	11	3	1	10	6	2	8			1	1
GSM9227436	1207	1754	500	170	314	108	138	12	23	23	115	154	40	50	2	167	5	2	6	8	4		1	123	16
GSM9227437	1749	964	1088	219	269	315	95	21	40	45	13	48	25	22	3	23		2	11	5	1		1	5	19
GSM9227438	2432	513	1099	82	616	98	24	27	65	17	2	3			1	1			4				2		4
GSM9227439	2201	802	733	148	509	227	48	33	90	33	21	16	18	3	3	22	8	13	4	17	15	2	5		20
GSM9227440	2687	448	936	124	337	103	62	44	156	44	19	5	8	2	5		3					2	2	1	3
GSM9227441	1623	170	587	77	2071	69	51	31	103	76	23	2	22	16	9	6	3		20	1		2	2	1	1	2
GSM9227442	2528	674	714	94	268	92	54	37	112	19	5	5	2	7	3	1	3	1	1	2				368
GSM9227443	2119	504	651	81	1137	139	49	36	91	18	110	5	12	2	3	6	3	3	2	2	5			6	5
GSM9227444	2383	348	643	52	1297	68	40	30	72	13	4	4		14	2	2	3		2	3	1	3			1
GSM9227445	1763	566	1014	61	1297	46	62	29	61	9	3	1			3	2	2							49		1
GSM9227446	2153	347	815	69	1399	46	37	17	60	22	3			3	2	3	1		1	2	1	3
GSM9227447	2794	221	566	73	1058	45	42	31	90	47	1		1	8	2	1	1	1		1		8
GSM9227448	2499	918	913	171	158	145	53	40	30	15	14	8	6	6	6	3	3	1	1	1
GSM9227449	2256	452	674	101	981	104	49	35	137	100	15	5	8	9		1	4	1	17		2	3	2	1		1
GSM9227450	1826	216	577	50	1850	47	41	18	81	64	13	3	6	10	3	2	2	1	25	2	3	1		1	2	1
GSM9227451	2205	605	696	107	732	265	26	43	50	25	9	15	20	8	8	3	8	3	3	7	1	1			10	5
GSM9227452	1489	1119	1057	153	642	267	70	25	28	3	40	23	18	11	2	27		2		9	3		1		2
GSM9227453	1799	739	534	290	432	328	79	31	21	14	289	37	137	21	3	185	4	1	2	21	19	2	1
GSM9227454	2396	351	768	75	1115	151	29	21	16	22	12	5	4	6		1	2	4	6	1	1			1
GSM9227455	3221	257	575	60	628	88	36	25	33	18	22	1	7	9	2	1		1	2	1		3
GSM9227456	2622	221	1450	65	440	41	31	21	26	8	5	1	3	12		4		1				1		40
GSM9227457	1970	103	920	70	1657	42	41	26	43	60	11	5	3	24	1			1	6	2	1	4		1
GSM9227458	1537	139	922	67	2036	60	29	20	24	51	10	6	11	18	2	3	7	2	30	3	2	8			1	1
GSM9227459	991	97	787	39	2780	50	37	18	33	41	23	2	10	7	2		5		41	2	5	3	6	10	1
GSM9227460	1521	1242	1436	67	208	83	36	25	16	14	37	12	17	6	1	3	5	1	5	5	2	1	2	205	17	1
GSM9227461	2343	508	1345	44	272	74	22	17	4	5	4	5	3	23		4		3	6	2	2	2			4	3
GSM9227462	2918	385	689	51	540	69	28	25	9	9	8	15	7	36	1	15	13	7	3	16	18	3	5		18	4
GSM9227463	2122	532	1439	69	539	47	20	25	30	11	20	5	3	17		3	1	2	5	1	3	6		87	3
GSM9227464	2891	288	883	56	469	38	42	20	36	13	3	3	2	6	4	2		1	5	2	2		1	2
GSM9227465	2171	446	398	59	1131	77	31	17	137	12	30	18	4	35	6	7	17	12		9	51	4	6		14	10

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
\|\|	STR D2 MSN	STR D2 MSN	`STR_D2_MSN`
\|\|	Astrocyte	Astrocyte	`Astrocyte`
\|\|	STR D1 MSN	STR D1 MSN	`STR_D1_MSN`
\|\|	CN ST18 GABA	CN ST18 GABA	`CN_ST18_GABA`
\|\|	Oligodendrocyte	Oligodendrocyte	`Oligodendrocyte`
\|\|	STR Hybrid MSN	STR Hybrid MSN	`STR_Hybrid_MSN`
\|\|	CN Cholinergic GABA	CN Cholinergic GABA	`CN_Cholinergic_GABA`
\|\|	STR SST CHODL GABA	STR SST CHODL GABA	`STR_SST_CHODL_GABA`
\|\|	Endo	Endo	`Endo`
\|\|	Pericyte	Pericyte	`Pericyte`
\|\|	F GABA	F GABA	`F_GABA`
\|\|	CN LHX8 GABA	CN LHX8 GABA	`CN_LHX8_GABA`
\|\|	STR RSPO2 GABA	STR RSPO2 GABA	`STR_RSPO2_GABA`
\|\|	OT Granular GABA	OT Granular GABA	`OT_Granular_GABA`
\|\|	SMC	SMC	`SMC`
\|\|	ACx MEIS2 GABA	ACx MEIS2 GABA	`ACx_MEIS2_GABA`
\|\|	OPC	OPC	`OPC`
\|\|	CN LAMP5 CXCL14 GABA	CN LAMP5 CXCL14 GABA	`CN_LAMP5_CXCL14_GABA`
\|\|	Lymphocyte	Lymphocyte	`Lymphocyte`
\|\|	CN LAMP5 LHX6 GABA	CN LAMP5 LHX6 GABA	`CN_LAMP5_LHX6_GABA`
\|\|	CN VIP GABA	CN VIP GABA	`CN_VIP_GABA`
\|\|	VLMC	VLMC	`VLMC`
\|\|	Microglia	Microglia	`Microglia`
\|\|	Ependymal	Ependymal	`Ependymal`
\|\|	COP	COP	`COP`
\|\|	Macrophage	Macrophage	`Macrophage`

Cell Type Probabilities

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

Showing ³⁸/₃₈ rows and ²⁶/₂₆ columns.

Sample	ACx MEIS2 GABA	Astrocyte	CN Cholinergic GABA	CN LAMP5 CXCL14 GABA	CN LAMP5 LHX6 GABA	CN LHX8 GABA	CN ST18 GABA	CN VIP GABA	COP	Endo	Ependymal	F GABA	Lymphocyte	Macrophage	Microglia	OPC	OT Granular GABA	Oligodendrocyte	Pericyte	SMC	STR D1 MSN	STR D2 MSN	STR Hybrid MSN	STR RSPO2 GABA	STR SST CHODL GABA	VLMC
GSM9227428	0.2	0.3	0.3		0.3	0.3	0.2	0.2	0.2	0.3	0.2	0.2	0.2	0.1	0.2	0.2	0.2	0.3	0.2	0.3	0.3	0.3	0.3	0.2	0.3	0.2
GSM9227429	0.2	0.3	0.4		0.3	0.3	0.3		0.4	0.2		0.2	0.2				0.2	0.4	0.2		0.3	0.4	0.3	0.3	0.3	0.2
GSM9227430	0.2	0.3	0.4			0.4	0.3			0.3	0.5	0.3				0.2	0.4	0.4	0.2	0.2	0.3	0.3	0.3	0.2	0.3	0.2
GSM9227431	0.2	0.2	0.3	0.3	0.2	0.3	0.3	0.2		0.2		0.2	0.2			0.2	0.4	0.3	0.2	0.2	0.3	0.3	0.3	0.2	0.3
GSM9227432	0.2	0.2	0.3	0.3	0.2	0.3	0.3	0.3	0.3	0.2	0.3	0.3	0.2	0.4	0.1	0.3	0.3	0.3	0.2	0.3	0.3	0.4	0.3	0.2	0.3	0.3
GSM9227433	0.3	0.2	0.4	0.3	0.5	0.3	0.3		0.3	0.2	0.3	0.3	0.2	0.2	0.3	0.2	0.3	0.5	0.2	0.3	0.3	0.4	0.3	0.3	0.3	0.2
GSM9227434	0.3	0.2	0.4	0.3	0.2	0.3	0.3	0.4	0.2	0.3	0.3	0.3	0.3	0.2	0.2	0.3	0.3	0.3	0.3	0.3	0.4	0.4	0.4	0.3	0.4	0.3
GSM9227435	0.3	0.3	0.4	0.2	0.3	0.2	0.3	0.2	0.1	0.3		0.2	0.3	0.2		0.2	0.3	0.4	0.2	0.2	0.3	0.4	0.3	0.3	0.4	0.3
GSM9227436	0.2	0.3	0.3	0.2	0.2	0.3	0.3	0.2	0.2	0.2	0.6	0.3	0.3		0.2	0.2	0.3	0.3	0.2	0.3	0.3	0.3	0.3	0.3	0.3
GSM9227437	0.2	0.2	0.3	0.3	0.2	0.3	0.3	0.3	0.2	0.2	0.2	0.2	0.2		0.1		0.2	0.3	0.2	0.2	0.3	0.3	0.3	0.3	0.3
GSM9227438	0.2	0.3	0.4			0.2	0.3		0.3	0.3		0.2	0.2		0.3			0.5	0.2	0.4	0.3	0.4	0.3		0.3
GSM9227439	0.2	0.3	0.3	0.3	0.3	0.2	0.3	0.2	0.2	0.2		0.2	0.2		0.2	0.2	0.2	0.3	0.2	0.3	0.3	0.4	0.3	0.3	0.3	0.2
GSM9227440		0.2	0.4			0.2	0.3		0.4	0.3	0.2	0.2			0.2	0.2	0.2	0.3	0.2	0.2	0.3	0.3	0.3	0.2	0.3	0.2
GSM9227441	0.2	0.2	0.4		0.3	0.2	0.3		0.3	0.3	0.1	0.2	0.2	0.3	0.3	0.2	0.2	0.5	0.2	0.3	0.3	0.3	0.3	0.2	0.4	0.3
GSM9227442	0.2	0.3	0.4	0.1	0.3	0.2	0.3			0.3	0.5	0.3	0.3			0.2	0.3	0.4	0.2	0.3	0.3	0.3	0.3	0.2	0.3
GSM9227443	0.2	0.3	0.4	0.3	0.2	0.2	0.3	0.2	0.4	0.2	0.4	0.2	0.3			0.2	0.6	0.4	0.2	0.3	0.3	0.3	0.3	0.2	0.3
GSM9227444	0.2	0.2	0.4		0.2	0.3	0.3	0.2	0.2	0.2		0.2	0.3			0.2	0.2	0.6	0.2	0.2	0.3	0.3	0.3		0.3	0.2
GSM9227445	0.3	0.3	0.4			0.2	0.3			0.3	0.3	0.2		0.3		0.2		0.5	0.2	0.3	0.3	0.3	0.2		0.3
GSM9227446	0.2	0.2	0.4		0.2		0.3	0.3		0.2		0.3	0.2			0.2	0.3	0.4	0.2	0.2	0.3	0.3	0.3		0.4	0.2
GSM9227447	0.2	0.2	0.4	0.2	0.3		0.3			0.2		0.2				0.2	0.2	0.5	0.2	0.2	0.3	0.3	0.3	0.4	0.3	0.2
GSM9227448	0.2	0.3	0.4	0.2	0.2	0.3	0.3			0.3		0.2	0.2			0.2	0.3	0.3	0.2	0.3	0.3	0.3	0.3	0.2	0.3
GSM9227449	0.2	0.2	0.4	0.2		0.2	0.3	0.2		0.2	0.2	0.2	0.2	0.3	0.3	0.3	0.2	0.5	0.2		0.3	0.3	0.3	0.2	0.3	0.2
GSM9227450	0.2	0.2	0.3	0.2	0.2	0.2	0.3	0.3	0.4	0.2	0.2	0.2	0.2	0.3		0.2	0.2	0.6	0.2	0.3	0.3	0.3	0.3	0.2	0.3	0.4
GSM9227451	0.2	0.2	0.4	0.3	0.2	0.2	0.3	0.3	0.2	0.3		0.2	0.2	0.3		0.2	0.3	0.4	0.2	0.3	0.3	0.3	0.3	0.2	0.3	0.2
GSM9227452	0.2	0.2	0.3	0.3	0.2	0.3	0.3	0.2	0.2	0.3		0.2			0.2		0.3	0.3	0.2	0.2	0.3	0.3	0.3	0.2	0.3
GSM9227453	0.2	0.2	0.3	0.3	0.2	0.2	0.2	0.2		0.2		0.2	0.2		0.2	0.2	0.3	0.3	0.2	0.3	0.3	0.4	0.4	0.2	0.3	0.2
GSM9227454	0.2	0.2	0.4	0.2	0.2	0.2	0.3	0.2		0.2	0.3	0.2	0.2			0.2	0.2	0.4	0.2		0.3	0.3	0.3	0.2	0.3
GSM9227455	0.2	0.2	0.3	0.3	0.2	0.2	0.3			0.2		0.2	0.2				0.2	0.3	0.2	0.3	0.3	0.4	0.3	0.2	0.3	0.2
GSM9227456	0.3	0.3	0.5	0.3		0.2	0.4			0.3	0.4	0.3					0.3	0.5	0.2		0.4	0.4	0.3	0.2	0.3	0.2
GSM9227457		0.2	0.4	0.3	0.2	0.2	0.3	0.2		0.2	0.2	0.2	0.2				0.3	0.4	0.2	0.3	0.3	0.3	0.3	0.2	0.4	0.2
GSM9227458	0.2	0.3	0.4	0.3	0.2	0.2	0.3	0.2	0.3	0.2		0.2	0.2	0.3		0.2	0.3	0.5	0.2	0.2	0.3	0.4	0.3	0.2	0.4	0.3
GSM9227459		0.3	0.4		0.2	0.2	0.3	0.2	0.3	0.3	0.4	0.2	0.2		0.4	0.2	0.2	0.5	0.2	0.3	0.3	0.4	0.3	0.3	0.4	0.2
GSM9227460	0.2	0.3	0.4	0.2	0.3	0.2	0.3	0.3	0.3	0.2	0.6	0.3	0.2	0.2	0.2	0.3	0.2	0.3	0.2	0.2	0.3	0.4	0.3	0.3	0.3	0.3
GSM9227461	0.2	0.3	0.4	0.3	0.2	0.2	0.3	0.2	0.3	0.2		0.3	0.2	0.3			0.3	0.4	0.3		0.3	0.4	0.3	0.3	0.3	0.3
GSM9227462	0.3	0.3	0.3	0.3	0.3	0.2	0.3	0.3	0.3	0.2		0.4	0.2	0.3	0.2	0.3	0.3	0.3	0.2	0.3	0.3	0.4	0.3	0.2	0.3	0.2
GSM9227463	0.3	0.2	0.4	0.2	0.4	0.3	0.3	0.3	0.3	0.2	0.4	0.2	0.2			0.3	0.3	0.4	0.2		0.3	0.4	0.3	0.2	0.3	0.2
GSM9227464	0.3	0.3	0.4	0.2	0.3	0.4	0.3	0.2		0.3	0.3	0.2	0.3		0.2		0.3	0.5	0.3	0.2	0.3	0.4	0.3	0.3	0.3
GSM9227465	0.2	0.3	0.3	0.2	0.2	0.2	0.3	0.2	0.3	0.2		0.2		0.2	0.2	0.3	0.3	0.4	0.2	0.3	0.3	0.4	0.3	0.3	0.3	0.3

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
\|\|	ACx MEIS2 GABA	ACx MEIS2 GABA	`ACx_MEIS2_GABA`
\|\|	Astrocyte	Astrocyte	`Astrocyte`
\|\|	CN Cholinergic GABA	CN Cholinergic GABA	`CN_Cholinergic_GABA`
\|\|	CN LAMP5 CXCL14 GABA	CN LAMP5 CXCL14 GABA	`CN_LAMP5_CXCL14_GABA`
\|\|	CN LAMP5 LHX6 GABA	CN LAMP5 LHX6 GABA	`CN_LAMP5_LHX6_GABA`
\|\|	CN LHX8 GABA	CN LHX8 GABA	`CN_LHX8_GABA`
\|\|	CN ST18 GABA	CN ST18 GABA	`CN_ST18_GABA`
\|\|	CN VIP GABA	CN VIP GABA	`CN_VIP_GABA`
\|\|	COP	COP	`COP`
\|\|	Endo	Endo	`Endo`
\|\|	Ependymal	Ependymal	`Ependymal`
\|\|	F GABA	F GABA	`F_GABA`
\|\|	Lymphocyte	Lymphocyte	`Lymphocyte`
\|\|	Macrophage	Macrophage	`Macrophage`
\|\|	Microglia	Microglia	`Microglia`
\|\|	OPC	OPC	`OPC`
\|\|	OT Granular GABA	OT Granular GABA	`OT_Granular_GABA`
\|\|	Oligodendrocyte	Oligodendrocyte	`Oligodendrocyte`
\|\|	Pericyte	Pericyte	`Pericyte`
\|\|	SMC	SMC	`SMC`
\|\|	STR D1 MSN	STR D1 MSN	`STR_D1_MSN`
\|\|	STR D2 MSN	STR D2 MSN	`STR_D2_MSN`
\|\|	STR Hybrid MSN	STR Hybrid MSN	`STR_Hybrid_MSN`
\|\|	STR RSPO2 GABA	STR RSPO2 GABA	`STR_RSPO2_GABA`
\|\|	STR SST CHODL GABA	STR SST CHODL GABA	`STR_SST_CHODL_GABA`
\|\|	VLMC	VLMC	`VLMC`

Spatial Neighbors

Cell type immediate neighborhood across samples.

Created with MultiQC

Squidpy Ligrec Interactions

Mean interaction across samples shown as no groups were specified.

Created with MultiQC

Moran I Interactions

Mean interaction across samples shown as no groups were specified.

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	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_LIGREC_ANALYSIS	anndata	`0.12.6`
	scanpy	`1.11.5`
	squidpy	`1.6.6.dev24+g32789aefd`
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	`24.10.4`
	STAPLE	`v2.2.2-gfbf88bd`

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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

Spatial Neighbors

Squidpy Ligrec Interactions

Moran I Interactions

Software Versions

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