Analysis Guides

Analysis of 10x Genomics data is full of possibilities. Here is a collection of introductions, tutorials, and blogs for data analysis beyond software developed by 10x Genomics. We hope these guides help you navigate your exciting analysis journey.

Introductions

Broad introductions to common data analysis topics.

Batch Effect Correction

Batch Effect Correction

Batch effects come from technical variation across samples. This can often be prevented with good experimental design. When it cannot, there are computational approaches that can help.

Batch effects come from technical variation across samples. This can often be prevented with good experimental design. When it cannot, there are computational approaches that can help.

Web Resources for Cell Type Annotation

Web Resources for Cell Type Annotation

The advantage of visualizing cell populations at single-cell resolutions has introduced us to the challenges of annotating cells. A growing number of annotation databases and tools are available to aid us in the process. In this article, we provide general guidance for a selected few to assist you with your research.

The advantage of visualizing cell populations at single-cell resolutions has introduced us to the challenges of annotating cells. A growing number of annotation databases and tools are available to aid us in the process. In this article, we provide general guidance for a selected few to assist you with your research.

Tutorials

Step-by-step example analysis covering a variety of topics.

Correcting Batch Effects in Visium Data

Correcting Batch Effects in Visium Data

Guided, step-by-step tutorial in R for correcting batch effects between two public 10x Genomics Visium datasets (mouse brain) using the Harmony algorithm, then importing corrected projections and clusters into the Loupe Browser.

Guided, step-by-step tutorial in R for correcting batch effects between two public 10x Genomics Visium datasets (mouse brain) using the Harmony algorithm, then importing corrected projections and clusters into the Loupe Browser.

Navigating 10x Genomics Barcoded BAM Files

Navigating 10x Genomics Barcoded BAM Files

The BAM file produced by the Ranger pipelines include standard SAM/BAM flags and several custom flags that can be used to mine information about alignment, annotation, counting, etc. This tutorial walks users through the process of identifying records in the BAM file that contribute to UMI counting.

The BAM file produced by the Ranger pipelines include standard SAM/BAM flags and several custom flags that can be used to mine information about alignment, annotation, counting, etc. This tutorial walks users through the process of identifying records in the BAM file that contribute to UMI counting.

Testing Microscope Image Compatibility with Space Ranger

Testing Microscope Image Compatibility with Space Ranger

Guides users through testing Loupe Browser and Space Ranger compatibility with images of various formats. Illustrates conversion to compatible TIFF in Fiji using multichannel CZI and multi-hue SVS images.

Guides users through testing Loupe Browser and Space Ranger compatibility with images of various formats. Illustrates conversion to compatible TIFF in Fiji using multichannel CZI and multi-hue SVS images.

Informatics Blogs

Tips, commentary, and highlights related to 10x Genomics data analysis.

Continuing Your Journey After Running Cell Ranger

Continuing Your Journey After Running Cell Ranger

Guidance on next steps after running Cell Ranger, including 10x Genomics tools and third-party tool analysis.

Guidance on next steps after running Cell Ranger, including 10x Genomics tools and third-party tool analysis.

Publication Highlight: Benchmarking scRNA-seq Batch Correction Methods

Publication Highlight: Benchmarking scRNA-seq Batch Correction Methods

Tran et al. performed comprehensive comparisons of 14 batch correction methods. Different methods performed best for 10x Genomics datasets with different characteristics.

Tran et al. performed comprehensive comparisons of 14 batch correction methods. Different methods performed best for 10x Genomics datasets with different characteristics.

10 Tips for Biologists Learning Bioinformatics

10 Tips for Biologists Learning Bioinformatics

Getting started in bioinformatics can feel overwhelming. In this article, you will find some tips and tricks that have helped us on this journey.

Getting started in bioinformatics can feel overwhelming. In this article, you will find some tips and tricks that have helped us on this journey.