10x Analysis Journey
Introductions
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
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 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 Visium datasets (mouse brain) using the Harmony algorithm, then importing corrected projections and clusters into the Loupe Browser.
Navigating 10x barcoded BAM files
Navigating 10x 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.
Informatics Blogs
Continuing your journey after running Cell Ranger
Continuing your journey after running Cell Ranger
Guidance on next steps after running Cell Ranger, including 10x tools and third-party tool analysis.
Guidance on next steps after running Cell Ranger, including 10x 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.