SCP Support
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Articles
Recent activity by SCP Support-
Spatial transcriptomics
Spatial transcriptomics visualizations are normal scatter plots that show how cells are arranged in 2d physical space, rather than how they may cluster by similarity based on an analysis. SCP allo...
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Key study files depend on unique NAMEs to enable visualizations
Single Cell Portal generates visualizations using information from three key study files: processed matrix, metadata and cluster files. This article covers: NAME Metadata file Cluster/spatial file...
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Reviewer access
Granting reviewer access Pre-publication studies often start as private studies. To grant reviewers access to a private study, SCP has a "Reviewer Access" feature that enables publication reviewers...
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Use the SCP accession URL in your publication
Include your SCP study URL in your paper to publicize your science! Researchers who read your paper can follow the link to your study, perform interactive visualization, and explore your findings. ...
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How SCP renders data in scatter plots
Single Cell Portal has special logic depending on the type of scatter plot to address issues surrounding over-plotting. Group-based annotations Any scatter plot that is displaying group-based annot...
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Link to your publication
External Resource links Researchers exploring studies in SCP often seek the following information in studies: Publication information SCP provides a way to add a button in the study summary to l...
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Commonly requested study details
Study summary content Researchers exploring studies in SCP often seek the following information in studies: A primary point of contact and email contact To handle privacy concerns, consider creat...
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Exploratory differential gene expression analysis
Exploratory differential expression (DE) analysis can be performed in Single Cell Portal to look for genes that drive differences between distinctly annotated clusters of cells in a study. For exam...
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Pathways
How does gene expression in a particular study relate to disease mechanisms and gene regulatory networks? Pathway search and visualization features in Single Cell Portal give insight into these bi...
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Bookmarks
Single Cell Portal enables the discovery and exploration of many datasets. Upon visiting SCP, you may find an interesting view of the data you'd like to return to or share with a colleague. Or you ...