Web application for exploration of large scale scRNA-seq datasets, upgraded to enable end-to-end interactive analysis.

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Project description

For the Data Science team

This fork implements some of the key features that have been highly requested by the data science team at CZBiohub.

Features include:

  • Hotkeys (SHIFT+? to see a tooltip describing all available hotkeys)
  • End-to-end interactive analysis and reembedding, with new embeddings hierarchically organized.
  • LIDAR graph interaction mode (the airplane) - Show an interactive tooltip describing the cells underneath your cursor. Very helpful for the color impaired or for large datasets with hundreds of labels.
  • Sankey plots
  • Leiden clustering
  • Label fusion and deletion
  • Interactive selection of data layer for expression visualization

Installation

The easiest way is to install from the precompiled pip distribution located in dist/. Clone this repo, activate your virtual environment of choice (conda or venv, typically), and install with:

pip install excellxgene

Ping me on slack (@Alec) if you have any questions!

Project details

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Maintainers
Avatar for keithcc from gravatar.com keithcc Avatar for rafael.gomez.s from gravatar.com rafael.gomez.s Avatar for tarashan from gravatar.com tarashan Avatar for yangjoon from gravatar.com yangjoon

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Release history Release notifications | RSS feed

2.9.6

2.9.5

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2.9.2

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broken

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unstable

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unstable

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unstable

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unstable

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unstable

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memory leakage with ray

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premature release

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width of volcanoplot bugged

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Sankey broken again

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Bug with scatter plots

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Windows pathing bug still present

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This version

1.0.5

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1.0.0

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