Exploratory CellxGene (ExCellxGene)

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
Many other quality-of-life improvements.

Patch notes (v1.2.5)

When displaying continuous metadata, cells with value zero are drawn as if they are unselected to send them to the background.
Category and geneset menus now have a new menu item to include/exclude zeros from the histograms. This is useful when the distributions are super zero-inflated.

Patch notes (v1.2.3)

Gene sets are now grouped based on their descriptions under collapsible headers.
Gene sets are now more compact, displaying 10 genes at a time with buttons to flip through pages.
Differential expression now calculates the top 100 genes.
A new button in the menubar allows you to calculate marker genes for all labels in a selected category.
Embeddings are now indented according to their hierarchical organization, and nested embeddings are collapsible.
Categorical labels are now sortable based on the currently displayed continuous medatada.
All preprocessing and reembedding parameters now have a tooltip.
Added a button to display hotkey menu to the menubar.
Various bugfixes.

Installation

Install miniconda if conda not available already:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O ~/miniconda.sh
bash ~/miniconda.sh -b -p $HOME/miniconda

Create and activate a new environment:

conda create -n cxg python=3.8
conda activate cxg

Install excellxgene with pip:

pip install excellxgene

If your operating system is CentOS, then you may run into issues installing dependencies that require up-to-date gcc or g++ compilers. Please install with the following and try reinstalling excellxgene with pip:

conda install -c conda-forge gcc cxx-compiler

Download the git repository to get the example datasets (assumes git is available, if not install it with conda install -c anaconda git)

git clone https://github.com/czbiohub/excellxgene
cd excellxgene

Datasets are stored in example-dataset

Launch excellxgene with:

excellxgene launch example-dataset

This should launch an excellxgene session with all the datasets in example-datasets/ loaded in.

If you're running excellxgene remotely, please launch with:

excellxgene launch example-datasets --host 0.0.0.0

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

Metadata

Release files for excellxgene 2.1.5

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for excellxgene 2.1.5
File	Size	Uploaded
excellxgene-2.1.5.tar.gz	6.9 MB	Jan 6, 2022	Details

Release files / excellxgene-2.1.5.tar.gz

Download URL	excellxgene-2.1.5.tar.gz
Size	6.9 MB
Tags	Source
SHA-256 checksum How to use checksums	`f6bc5463af9aec92ac1a37fdc4e98a92e44bf591da68ee0cd5cbc86f3b793d10`
BLAKE2b-256 checksum How to use checksums	`3285e36ed3c8bfade3048fe5ff0f8c5c9fc84ea7c3b7e3512fb7bfc9718b8832`
Upload date	Jan 6, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/3.7.1 importlib_metadata/4.10.0 pkginfo/1.8.2 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.3 CPython/3.8.12`