CaltechAUTHORS
Published July 4, 2021 | Version Submitted
Discussion Paper Open

Single cell tools for WormBase

Creators

Abstract

We present two web apps for interactively performing common tasks with single cell RNA sequencing data: scdefg for interactive differential expression and wormcells-viz for visualization of gene expression. We made these tools available with public C. elegans datasets curated by WormBase at single-cell.wormbase.org. They can also be readily deployed for use with any other datasets using the source code available at github.com/WormBase/scdefg and at github.com/WormBase/wormcells-viz.

Additional Information

The copyright holder has placed this preprint in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or adapt this material for any purpose without crediting the original authors. This version posted July 4, 2021. The authors would like to thank Paulo Nuin for reviewing the code, Tom Morrell for assistance with CaltechData, and Valentine Svensson for suggestions on the manuscript. This work was supported by grants NIH U24HG010859 and NIH U24HG002223.

Attached Files

Submitted - 2021.07.04.451030v1.full.pdf

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Additional details

Identifiers

Eprint ID
109773
Resolver ID
CaltechAUTHORS:20210712-143510822

Related works

Describes
https://single-cell.wormbase.org/ (URL)
https://github.com/WormBase/scdefg (URL)
https://github.com/WormBase/wormcells-viz (URL)
https://github.com/WormBase/anndata-wrangling (URL)
Is published in
https://authors.library.caltech.edu/records/4a7mt-ccj86 (URL)

Funding

NIH
U24HG010859
NIH
U24HG002223

Dates

Created
2021-07-12
Created from EPrint's datestamp field
Updated
2021-11-16
Created from EPrint's last_modified field

Caltech Custom Metadata

Caltech groups
WormBase, Division of Biology and Biological Engineering (BBE)