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CellBender fails on my data with "not enough empty droplets" error even though I set `--low-count-threshold` to 2. The error & log itself are a bit weird (look at the scale of nUMI filtered). I get th…
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Hi,
I would like to have some help: I'm running CellBender on a "problematic" sample (trial of new nuclei isolation protocol , resulted in lower quality). We know that many cells need to be discard…
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Hi, I am running into IndexError and ValueError errors for some samples after traning.
I run the following command with us.gcr.io/broad-dsde-methods/cellbender:20230403:
cellbender remove-backgrou…
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### To triage
- [x] [The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages.](https://contribute.data.humancellatlas.org/projects/detail?uuid=4aee283b-ce74-4da6-ade5-d3d…
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New Projects (10)
1. [A Single-Cell Transcriptome Atlas of Glia Diversity in the Human Hippocampus across the Lifespan and in Alzheimer’s Disease](https://data.humancellatlas.org/explore/projects/258c…
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https://broadinstitute.github.io/2020_scWorkshop/
? https://nbisweden.github.io/workshop-scRNAseq/schedule.html
https://azimuth.hubmapconsortium.org/
Single-nucleus and single-cell transcrip…
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Researchers need to be aware of which data are single-cell vs single-nucleus so that they can take special care to ensure proper integration.
Most contributors don't provide it automatically because …
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Hi Alevin-fry developers,
I am currently working on a combinatory indexing scRNA-seq dataset. And given that my dataset would have many ambient RNA, I would like to use the empty droplets for back…
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Add repo description. We could use this as an opportunity say that the pipeline caters to both external and Data Lab users.
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As mentioned in #1, we would like to have control datasets that represent a mix of tissues to compare data integration methods. We have a variety of tissue types that are represented in ScPCA so want …