MultiQC Report

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/9c/2553b551000879f5f2747f4fc4b036

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

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
B-cells_compartment	AnnData	54934.0	36503.0	True	True	B-cells_compartment	/data/analysis/data_becavin/checkatlas_test/tuto/data1/B-cells_compartment.h5ad
Fetal	AnnData	27203.0	32828.0	True	True	Fetal	/data/analysis/data_becavin/checkatlas_test/tuto/data1/Fetal.h5ad
Tabula_Sapiens_Endothelial	AnnData	31691.0	58559.0	True	True	Tabula_Sapiens_Endothelial	/data/analysis/data_becavin/checkatlas_test/tuto/data1/Tabula_Sapiens_Endothelial.h5ad

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

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 ¹⁰/₁₀ rows and ²/₂ columns.

Sample Name	obs	davies_bouldin
B-cells_compartment_Manually_curated_celltype	Manually_curated_celltype	1.3
B-cells_compartment_cell_type	cell_type	1.1
B-cells_compartment_cell_type_ontology_term_id	cell_type_ontology_term_id	1.1
Fetal_author_cell_type	author_cell_type	2.1
Fetal_cell_type	cell_type	1.9
Fetal_cell_type_ontology_term_id	cell_type_ontology_term_id	1.9
Fetal_orig.ident	orig.ident	23.9
Fetal_seurat_clusters	seurat_clusters	2.0
Tabula_Sapiens_Endothelial_cell_type	cell_type	4.5
Tabula_Sapiens_Endothelial_cell_type_ontology_term_id	cell_type_ontology_term_id	4.5

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

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 ⁷/₇ rows and ³/₃ columns.

Sample Name	Reference	obs	rand_index
B-cells_compartment_cell_type	Manually_curated_celltype	cell_type	1.0
B-cells_compartment_cell_type_ontology_term_id	Manually_curated_celltype	cell_type_ontology_term_id	1.0
Fetal_cell_type	author_cell_type	cell_type	0.7
Fetal_cell_type_ontology_term_id	author_cell_type	cell_type_ontology_term_id	0.7
Fetal_orig.ident	author_cell_type	orig.ident	0.1
Fetal_seurat_clusters	author_cell_type	seurat_clusters	0.4
Tabula_Sapiens_Endothelial_cell_type_ontology_term_id	cell_type	cell_type_ontology_term_id	1.0

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

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 ⁷/₇ rows.

Sample Name	obsm
B-cells_compartment_X_umap	X_umap
Fetal_X_pca	X_pca
Fetal_X_umap	X_umap
Tabula_Sapiens_Endothelial_X_pca	X_pca
Tabula_Sapiens_Endothelial_X_scvi	X_scvi
Tabula_Sapiens_Endothelial_X_scvi_umap	X_scvi_umap
Tabula_Sapiens_Endothelial_X_umap	X_umap

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

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	uns
B-cells_compartment	`donor_id` `Predicted_labels_CellTypist` `Majority_voting_CellTypist` `Manually_curated_celltype` `assay_ontology_term_id` `cell_type_ontology_term_id` `development_stage_ontology_term_id` `disease_ontology_term_id` `self_reported_ethnicity_ontology_term_id` `is_primary_data` `organism_ontology_term_id` `sex_ontology_term_id` `tissue_ontology_term_id` `suspension_type` `cell_type` `assay` `disease` `organism` `sex` `tissue` `self_reported_ethnicity` `development_stage`	`X_umap`	`gene_symbols` `feature_is_filtered` `feature_name` `feature_reference` `feature_biotype`	`cell_type_ontology_term_id_colors` `default_embedding` `development_stage_ontology_term_id_colors` `schema_version` `sex_ontology_term_id_colors` `title`
Fetal	`orig.ident` `nCount_RNA` `nFeature_RNA` `seurat_clusters` `donor_id` `Stage` `Selection` `compartment` `age` `CnT` `DTLH` `UBCD` `SSBpr` `End` `MSC` `RVCSB` `SSBpod` `SSBm.d` `ICa` `ErPrT` `ICb` `NPC` `Pod` `annotCell` `author_cell_type` `cell_type_ontology_term_id` `disease_ontology_term_id` `self_reported_ethnicity_ontology_term_id` `development_stage_ontology_term_id` `tissue_ontology_term_id` `sex_ontology_term_id` `organism_ontology_term_id` `is_primary_data` `assay_ontology_term_id` `suspension_type` `cell_type` `assay` `disease` `organism` `sex` `tissue` `self_reported_ethnicity` `development_stage`	`X_pca` `X_umap`	`vst.mean` `vst.variance` `vst.variance.expected` `vst.variance.standardized` `vst.variable` `feature_is_filtered` `feature_name` `feature_reference` `feature_biotype`	`schema_version` `title`
Tabula_Sapiens_Endothelial	`tissue_in_publication` `assay_ontology_term_id` `donor_id` `anatomical_information` `n_counts_UMIs` `n_genes` `cell_ontology_class` `free_annotation` `manually_annotated` `compartment` `sex_ontology_term_id` `is_primary_data` `organism_ontology_term_id` `disease_ontology_term_id` `self_reported_ethnicity_ontology_term_id` `development_stage_ontology_term_id` `cell_type_ontology_term_id` `tissue_ontology_term_id` `suspension_type` `cell_type` `assay` `disease` `organism` `sex` `tissue` `self_reported_ethnicity` `development_stage`	`X_pca` `X_scvi` `X_scvi_umap` `X_umap`	`feature_type` `ensemblid` `highly_variable` `means` `dispersions` `dispersions_norm` `mean` `std` `feature_is_filtered` `feature_name` `feature_reference` `feature_biotype`	`_scvi` `_training_mode` `default_embedding` `dendrogram_cell_type_tissue` `dendrogram_computational_compartment_assignment` `dendrogram_consensus_prediction` `dendrogram_tissue_cell_type` `donor_id_colors` `donor_method_colors` `hvg` `method_colors` `neighbors` `schema_version` `sex_colors` `tissue_in_publication_colors` `title` `umap`

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

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/data1/

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: stoic_pauling
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/data1/
outdir: N/A

v1.15.dev0

MultiQC Toolbox

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Tool Citations

About MultiQC

Checkatlas Qc Report

Checkatlas Umap Report

CheckAtlas

Atlas overview

QC total_counts

QC n_genes_by_counts

QC pct_counts_mt

Classification metrics

Annotation metrics

Dimensionality reduction metrics

Atlas object explorer

nf-core/checkatlas Methods Description

Methods

References

Notes:

nf-core/checkatlas Software Versions

nf-core/checkatlas Workflow Summary

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

Atlas overview

Table Srzu: Columns

QC total_counts

QC n_genes_by_counts

QC pct_counts_mt

Classification metrics

Table Nfhe: Columns

Annotation metrics

Table Wqdp: Columns

Dimensionality reduction metrics

Table Yjze: Columns

Atlas object explorer

Table Meax: 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