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Seurat.IntegrateData (v3) Summary References Technical Notes Parameters Output Files License Platform Dependencies Version Comments
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Seurat.IntegrateData (v3)

Description: GenePattern module which implements the batch correction algorithm derived from the Seurat software package (Seurat version 3.2.0).

Authors: Jonathan Zamora and Edwin F. Juárez, UCSD

Contact: Forum Link

Algorithm Version: Seurat 3.2.0

Summary

The Seurat.IntegrateData Module integrates (corrects for batch effects) multiple single-cell datasets and identifies shared cell states that are present across different datasets, regardless of their origin. Once the Module integrates these datasets, the returned object will contain a new Assay that holds an integrated/batch-corrected expression matrix for all cells. The resultant batch-corrected expression matrix can then be used for downstream analyses and visualizations.

References

"Seurat V3 Paper:" Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM 3rd, Hao Y, Stoeckius M, Smibert P, Satija R. Comprehensive Integration of Single-Cell Data. Cell. 2019 Jun 13;177(7):1888-1902.e21. doi: 10.1016/j.cell.2019.05.031. Epub 2019 Jun 6. PMID: 31178118; PMCID: PMC6687398.

Satija Lab

Seurat

Technical Notes

This module runs in the Docker container tagged genepattern/seurat-suite\:4.0.3.

GitHub repository for this module's code & version: https://github.com/genepattern/Seurat.IntegrateData/tree/v3

Parameters

Name Description
input_files Gene expression matrices (columns are cell IDs and rows are genes) stored in a .txt or one Seurat Object (.rds) file per batch. If your files are in 10x Genomics (Cell Ranger) format or stored in a .tar, or .gz file, please use the Seurat.QC module to pre-process your data and then use the .txt or .rds output from Seurat.QC in this module. For sample data see test data file 1 and test data file 2.
use_batch_names (default = TRUE) Map each input file to Batch Numbers beginning with Batch 1 and going up to Batch n where n represents the number of input files. When set to FALSE, the batch names will be set to the file names.
ncomps (default = 50) The number of principal components to be used in the Principal Component Analysis (PCA) for batch correction.
nCount_RNA (default = TRUE) Whether or not the batch correction script will produce a violin plot of the number of molecules detected within a cell for our single-cell datasets.
nFeature_RNA (default = TRUE) Whether or not the batch correction script will produce a violin plot of the number of genes detected within each cell of our single-cell datasets.
output_file_name (default = 'batch_correction_results') Base name for the .pdf and .rds output files.

Output Files

  1. batch_correction_log.txt
    • This .txt file contains a log of each process carried out during the batch correction script's execution.
  2. output_file_name.rds
    • This .rds file can be used on another one of GenePattern's Seurat suite modules, such as the Seurat.Clustering module.
    • It contains an integrated / batch-corrected expression matrix for all cells present in the input files.
    • Note: This file inherits its name from the output_file_name parameter listed above.
  3. output_file_name.pdf
    • This .pdf file contains both a UMAP plot and Violin plot of the integrated Seurat Objects that are derived from gene expression datasets.
    • Additionally, the first page will display a batch mapping table. In short, this table maps input files to numbered batches, starting at Batch 1 and going up to Batch n where n represents the number of input files given to the script.
    • Note: This file inherits its name from the output_file_name parameter listed above.

License

Seurat.IntegrateData is distributed under a modified BSD license available at https://github.com/genepattern/Seurat.IntegrateData/blob/v3/LICENSE.

Platform Dependencies

Task Type CPU Type Operating System Language
Any Any R 4.0.2

Version Comments

Version Release Date Description
3 Mar. 12th, 2021 Input types now include .rds, tsv, and .txt files. Output shows data before the batch correction (in addition to post batch correction).
2 Mar. 3rd, 2021 Introduced updates to parameters, program structure, and output format.
1 Nov. 4th, 2020 Initial Release of Seurat.BatchCorrection.