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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 1.15.dev0

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/ewels/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

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

This report has been generated by the nf-core/checkatlas analysis pipeline. For information about how to interpret these results, please see the documentation.

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Report generated on 2023-07-22, 01:19 based on data in: /data/analysis/data_becavin/checkatlas_test/tuto/work/f5/face1e71460f5c293919bd7810cf22

Checkatlas Qc Report

Custom content with all qc plots found in your atlases

Checkatlas Umap Report

Custom content with all reductions plots found in your atlases

Checkatlas Tsne Report

Custom content with all reductions plots found in your atlases

CheckAtlas

CheckAtlas A one-liner tool for quality control of your single-cell atlases.

Atlas overview

Overview of your single-cell atlases

Showing ³/₃ rows and ⁷/₇ columns.

Sample Name	AtlasFileType	NbCells	NbGenes	AnnData.raw	AnnData.X	File_extension	File_path
pbmc_3k_cellranger	Cellranger >= v3	5025.0	33538.0	False	True	pbmc_3k_cellranger	/data/analysis/data_becavin/checkatlas_test/tuto/data3/pbmc_3k_cellranger/outs/filtered_feature_bc_matrix.h5
pbmc_3k_scanpy	AnnData	2638.0	1838.0	True	True	pbmc_3k_scanpy	/data/analysis/data_becavin/checkatlas_test/tuto/data3/pbmc_3k_scanpy.h5ad
pbmc_3k_seurat	Seurat	2638.0	13714.0	False	True	.rds	/data/analysis/data_becavin/checkatlas_test/tuto/data3/pbmc_3k_seurat.rds

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

Sort	Column	Description	ID	Scale
\|\|	AtlasFileType	AtlasFileType	`AtlasFileType`	None
\|\|	NbCells	NbCells	`NbCells`	None
\|\|	NbGenes	NbGenes	`NbGenes`	None
\|\|	AnnData.raw	AnnData.raw	`AnnData.raw`	None
\|\|	AnnData.X	AnnData.X	`AnnData.X`	None
\|\|	File_extension	File_extension	`File_extension`	None
\|\|	File_path	File_path	`File_path`	None

QC total_counts

QC of your atlases log10(Cellrank vs total-counts.

QC n_genes_by_counts

QC of your atlases log10(Cellrank vs n_genes_by_counts.

QC pct_counts_mt

QC of your atlases log10(Cellrank vs pct_counts_mt.

Classification metrics

Quality control metrics calculated on your atlases.

Showing ³/₃ rows and ²/₂ columns.

Sample Name	obs	davies_bouldin
pbmc_3k_scanpy_louvain	louvain	0.6
pbmc_3k_seurat_RNA_snn_res.0.5	RNA_snn_res.0.5	0.6
pbmc_3k_seurat_seurat_clusters	seurat_clusters	0.6

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

Sort	Visible	Group	Column	Description	ID	Scale
\|\|		metric_cluster_table	obs	obs	`obs`	None
\|\|		metric_cluster_table	davies_bouldin	davies_bouldin	`davies_bouldin`	None

Annotation metrics

Quality control metrics calculated on your atlases.

Showing ¹/₁ rows and ³/₃ columns.

Sample Name	Reference	obs	rand_index
pbmc_3k_seurat_seurat_clusters	RNA_snn_res.0.5	seurat_clusters	1.0

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

Sort	Column	Description	ID	Scale
\|\|	Reference	Reference	`Reference`	None
\|\|	obs	obs	`obs`	None
\|\|	rand_index	rand_index	`rand_index`	None

Dimensionality reduction metrics

Quality control metrics calculated on your atlases.

Showing ⁶/₆ rows.

Sample Name	obsm
pbmc_3k_scanpy_X_draw_graph_fr	X_draw_graph_fr
pbmc_3k_scanpy_X_pca	X_pca
pbmc_3k_scanpy_X_tsne	X_tsne
pbmc_3k_scanpy_X_umap	X_umap
pbmc_3k_seurat_pca	pca
pbmc_3k_seurat_umap	umap

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

Sort	Visible	Group	Column	Description	ID	Scale
\|\|			obsm	obsm	`obsm`	None

Atlas object explorer

Exploration of your Atlas object (Scanpy, Cellanger, Seurat)

Showing ³/₃ rows and ⁵/₅ columns.

Sample Name	atlas_obs	obsm	var	varm	uns
pbmc_3k_cellranger			`gene_ids` `feature_types` `genome`
pbmc_3k_scanpy	`n_genes` `percent_mito` `n_counts` `louvain`	`X_pca` `X_tsne` `X_umap` `X_draw_graph_fr`	`n_cells`	`PCs`	`draw_graph` `louvain` `louvain_colors` `neighbors` `pca` `rank_genes_groups`
pbmc_3k_seurat	`orig.ident` `nCount_RNA` `nFeature_RNA` `percent.mt` `RNA_snn_res.0.5` `seurat_clusters`	`pca` `umap`

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

Sort	Group	Column	Description	ID	Scale
\|\|	adata_table	atlas_obs	atlas_obs	`atlas_obs`	None
\|\|	adata_table	obsm	obsm	`obsm`	None
\|\|	adata_table	var	var	`var`	None
\|\|	adata_table	varm	varm	`varm`	None
\|\|	adata_table	uns	uns	`uns`	None

nf-core/checkatlas Methods Description

Suggested text and references to use when describing pipeline usage within the methods section of a publication.

Methods

Data was processed using nf-core/checkatlas v1.0dev of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

The pipeline was executed with Nextflow v23.04.1 (Di Tommaso et al., 2017) with the following command:

nextflow run nf-core-checkatlas -r dev --path /data/analysis/data_becavin/checkatlas_test/tuto/data3/

References

Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192

Notes:

If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

nf-core/checkatlas Software Versions

are collected at run time from the software output.

Process Name	Software	Version
`CUSTOM_DUMPSOFTWAREVERSIONS`	`python`	`3.10.12`
	`yaml`	`6.0.1`
`LIST_CELLRANGER_ATLASES`	`checkatlas`	`0.3.9`
`LIST_SCANPY_ATLASES`	`checkatlas`	`0.3.9`
`LIST_SEURAT_ATLASES`	`checkatlas`	`0.3.9`
`Workflow`	`Nextflow`	`23.04.1`
	`nf-core/checkatlas`	`1.0dev`

nf-core/checkatlas Workflow Summary

- this information is collected when the pipeline is started.

Core Nextflow options

revision: dev
runName: awesome_meitner
launchDir: /data/analysis/data_becavin/checkatlas_test/tuto
workDir: /data/analysis/data_becavin/checkatlas_test/tuto/work
projectDir: /home/becavin/.nextflow/assets/becavin-lab/nf-core-checkatlas
userName: becavin
profile: standard
configFiles: N/A

Input/output options

path: /data/analysis/data_becavin/checkatlas_test/tuto/data3/
outdir: N/A

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About MultiQC

Checkatlas Qc Report

Checkatlas Umap Report

Checkatlas Tsne Report

CheckAtlas

Atlas overview

Table Xzya: Columns

QC total_counts

QC n_genes_by_counts

QC pct_counts_mt

Classification metrics

Table Scwg: Columns

Annotation metrics

Table Ucja: Columns

Dimensionality reduction metrics

Table Civs: Columns

Atlas object explorer

Table Xacz: Columns

nf-core/checkatlas Methods Description

Methods

References

Notes:

nf-core/checkatlas Software Versions

nf-core/checkatlas Workflow Summary

v1.15.dev0

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