spaceranger count
pipeline for generating feature-barcode matrices, identifying clustering, and performing differential gene expression from Visium data. We have adapted spaceranger count
to read and write data to your Mantle Database.
spatial-experiment
data type. Expand to view the properties of spatial-experiment
entities:
Properties
image
, darkimage
, colorizedimage
, or cytaimage
.Used as an input to Spaceranger Count as --<image_type> <image>
.See the Spaceranger Count documentation for more information.slide
input to Spaceranger Count. See the Spaceranger Count documentation for more information.loupe-alignment
input to Spaceranger Count. See the Spaceranger Count documentation for more information.area
input to Spaceranger Count. See the Spaceranger Count documentation for more information.Sudmeier, et al. (2022) “Distinct phenotypic states and spatial distribution of CD8+ T cell clonotypes in human brain metastases.” Cell Reports Medicine, 3(5), 100620To perform sequence alignment, a reference genome is needed. 10x has references available for human (
GRCH38-2020-A
) and mouse (mm10-2020-A
) genomes. They are available in your Mantle Database as spatial-reference
entities.
Depending on your experimental workflow, you may also need a spatial
probe file for data processing. 10x also has probesets available for
human and mouse, which are available in your Mantle Database as spatial-probes
entities.
spaceranger-count
pipeline adapts the 10x Genomics spaceranger count pipeline to allow it to take a Mantle spatial-experiment entity as input and to create a spaceranger-count-outputs
entity with the results directory. Additionally, when you run the Mantle spaceranger-count
pipeline, many of the results files can be previewed on the run page, including the an interactive pipeline report. All pipeline results files can also be browsed on the pipeline run page. Learn more about the pipeline in the 10x Genomics spaceranger count documentation.