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

Export Plots

Images
Data

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

Save Settings

You can save the toolbox settings for this report to the browser.

Load Settings

Choose a saved report profile from the dropdown box below:

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 1.15.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.

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 2023-07-22, 02:21 based on data in: /data/analysis/data_becavin/checkatlas_test/tuto/work/65/9ba8bb82797022b592961641925d3d

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 ⁴/₄ rows and ⁷/₇ columns.

Sample Name	AtlasFileType	NbCells	NbGenes	AnnData.raw	AnnData.X	File_extension	File_path
pbmc_3k_68k_integrated	AnnData	700.0	208.0	True	True	pbmc_3k_68k_integrated	/data/analysis/data_becavin/checkatlas_test/tuto/data4/pbmc_3k_68k_integrated.h5ad
pbmc_3k_68k_integrated_checkatlas_summ	Scanpy	700.0	208.0	True	True	.h5ad	/pbmc_3k_68k_integrated.h5ad
pbmc_3k_v1	Cellranger < v3	2700.0	32738.0	False	True	pbmc_3k_v1	/data/analysis/data_becavin/checkatlas_test/tuto/data4/pbmc_3k_v1/outs/filtered_gene_bc_matrices/hg19/matrix.mtx
pbmc_68k_v1	Cellranger < v3	68579.0	32738.0	False	True	pbmc_68k_v1	/data/analysis/data_becavin/checkatlas_test/tuto/data4/pbmc_68k_v1/outs/filtered_matrices_mex/hg19/matrix.mtx

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

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 ²/₂ rows and ²/₂ columns.

Sample Name	obs	davies_bouldin
pbmc_3k_68k_integrated_louvain	louvain	0.8
pbmc_3k_v1_cellranger_kmeans_10	cellranger_kmeans_10	1.7

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

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

Dimensionality reduction metrics

Quality control metrics calculated on your atlases.

Showing ³/₃ rows.

Sample Name	obsm
pbmc_3k_68k_integrated_X_pca	X_pca
pbmc_3k_68k_integrated_X_umap	X_umap
pbmc_3k_68k_integrated_rep	rep

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

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_68k_integrated	`bulk_labels` `n_genes` `percent_mito` `n_counts` `S_score` `G2M_score` `phase` `louvain`	`X_pca` `X_umap` `rep`	`n_counts` `means` `dispersions` `dispersions_norm` `highly_variable`	`PCs`	`bulk_labels_colors` `louvain` `louvain_colors` `neighbors` `pca` `rank_genes_groups`
pbmc_3k_v1	`cellranger_kmeans_10`		`gene_ids`
pbmc_68k_v1	`cellranger_kmeans_10`		`gene_ids`

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

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/data4/

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: condescending_yonath
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/data4/
outdir: N/A

Toggle navigation v1.15.dev0

MultiQC Toolbox

Apply Highlight Samples

Apply Rename Samples

Apply Show / Hide Samples

Export Plots

Choose Plots

Save Settings

Load Settings

Tool Citations

About MultiQC

Checkatlas Qc Report

Checkatlas Umap Report

Checkatlas Tsne Report

CheckAtlas

Atlas overview

Table Twzn: Columns

QC total_counts

QC n_genes_by_counts

QC pct_counts_mt

Classification metrics

Table Vyma: Columns

Dimensionality reduction metrics

Table Hdry: Columns

Atlas object explorer

Table Ptor: Columns

nf-core/checkatlas Methods Description

Methods

References

Notes:

nf-core/checkatlas Software Versions

nf-core/checkatlas Workflow Summary

v1.15.dev0

Highlight Samples

Rename Samples

Show / Hide Samples