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Sharing data is a crucial step in the lifecycle of a research project. But in spite of its value, this step can be time-consuming, particularly when you have to re-format your data before sharing it to an online repository like Single Cell Portal.
To reduce this burden, we’ve updated the file types that we accept for SCP studies. You can now create a Single Cell Portal study by uploading an .h5ad file containing an AnnData object. This should speed up the data contribution process by bridging the gap between the files that you work with when analyzing your data, and the files that you ultimately share with the research community. In addition, uploading AnnData to SCP will make it easier for other researchers to incorporate your data into their own analyses. While this change most directly impacts researchers who work in Scanpy, we hope that...
Exploring Differential Expression on Single Cell Portal October 7, 2022
Single-cell genomics gives researchers the power to interrogate the cell state of individual cells within a sample. This allows us to ask questions like, “how are different cell types affected by HIV?” and “which genetic programs are activated in cancer cells?” In investigating these questions, researchers often seek out differences in genetic expression across different groups of cells. To make it easier to spot these differences, Single Cell Portal now supports exploratory differential expression (DE) analyses for some datasets. This tool will help our users get a quick impression of the genes that distinguish between cell groups of interest, which can help verify cell annotations and inspire more rigorous follow-up work.
How does it work?
When you visit a study where this tool is available, you’ll see a “Differential Expression” button on the right-hand panel of the study’s ‘Explore’ tab.
After clicking that button, you can select a target annotation label...
Search across Data Portals in SCP March 22, 2022
Imagine you’re a researcher who’s interested in a specific topic within single-cell genomics – for example, HIV. To make your own research more thoughtful and impactful, it’s often useful to survey the existing datasets that involve HIV, to get a sense of what questions people are asking about HIV, and what the answers are so far. Or, you might be interested in gathering data on a specific cell type or organ. Gathering data of the same type, across multiple datasets, could help you build a cohort of data – you’ll then be able to run analyses across these datasets, with more statistical power to pick up small effects than if you were to analyze a single dataset. Doing so also allows you to find results that are more robust to the smaller details that set studies apart, such as the specific organisms that were sampled.
While gathering data from...
Better Color Scales for Gene Expression Plots December 9, 2021
Which color scale do you think that SCP should use by default? Take this 2-minute survey to let us know!
One of the Single Cell Portal’s goals is to build interactive plots that make it easy for scientists to explore the patterns in single-cell data. Given that, we’re always looking for ways to make our plots easier to interpret. As anyone who has made a paper figure can attest, there is a real art to this -- how do you make the data “sing” so that a viewer can instantly see the interesting patterns that it holds, while remaining honest about the complexity and noise in the data? Recently, we made some changes that improve the data’s ability to sing on SCP. Specifically, we updated the color scales that we use to plot gene expression data.
To understand the art behind plotting gene expression data well, it’s useful...
Study collections organize data by consortium or topic October 22, 2021
Have you ever visited the Single Cell Portal to search for interesting data, and gotten lost in all of the studies? Or, have you ever wished that you could easily point another researcher toward all of the data that you have on SCP, without sending them a separate link for each study?
If either of these stories sounds familiar, you can now take advantage of SCP's study collections. Collections are curated sets of studies that share a common topic or research group. If you've come to SCP to learn more about a specific research topic or group, browse through these collections to narrow your search down to the studies you're most likely to be interested in. And if you -- or your lab -- have several studies in SCP, you can create a collection in order to share your work more easily. Creating a collection simply opens a separate...
Anonymous Reviewer Access to SCP Studies October 22, 2021
Submitting your findings for publication can be one of the most stressful stages in the research lifecycle. Often, this is because the submission process requires you to manage several logistical tasks beyond the actual paper-writing. For example, more and more journals require a link to a repository where reviewers can explore your data as they comb through your manuscript. However, you might not be ready to share your data with the world until the paper has passed this review.
To ease this process, we’ve created a way to grant reviewers anonymous access to your SCP study while it is still private. Once you’ve activated access for reviewers, SCP will generate a unique URL and PIN, which your reviewers can use to visualize and explore your data (but not download it). You can also control when this access expires, or reset the access information at any time...
Upload and Explore Spatial Transcriptomics Data October 20, 2021
SCP now supports spatial transcriptomics data! These data help researchers understand how patterns in genetic expression or cell types are distributed in the tissue. For example, are cells with similar genetic expression profiles clustered close together in the tissue, or dispersed throughout? You can explore these spatial distributions alongside other plots, like gene expression clustering plots -- check out an example study here!
If you have spatial transcriptomics data to share through SCP, you can upload the spatial coordinates of your samples through our upload wizard.
This look into spatial data is part of a series of announcements where we’ll shine a light on previously-hidden features of SCP. These will include:
- Granting study access to anonymous reviewers
- Study “collections”
- An ideogram viewer to discover related genes
- Selecting customized subsets of data from a plot
- Our new requirement to include raw counts matrices when you upload data
- Adding images to your study's description
We’ll also highlight...