Skip to main content

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

Project description

Exploratory CellxGene (ExCellxGene)

Video vignettes to come!

V2.6.3

In the latest version, the internal file system used by excellxgene has been restructured. As a result, launching excellxgene on a dataset you have previously worked with will create a new folder with none of your previous work. You will need to migrate your work to the new version of excellxgene. The easiest way to do this is with the following:

  1. Create a new conda environment (same instructions as in the installation section).
  2. Pip install excellxgene==2.6.3
  3. Launch the new version of excellxgene.
  4. Upload the metadata/genesets/etc downloaded from the old version of excellxgene to the new version.

Installation

  1. 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
  1. Create and activate a new environment:
conda create -n cxg python=3.8
conda activate cxg
  1. 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
  1. 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

  1. 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!

Project details


Release history Release notifications | RSS feed

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

excellxgene-2.8.8.tar.gz (7.3 MB view details)

Uploaded Source

File details

Details for the file excellxgene-2.8.8.tar.gz.

File metadata

  • Download URL: excellxgene-2.8.8.tar.gz
  • Upload date:
  • Size: 7.3 MB
  • Tags: Source
  • Uploaded using 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

File hashes

Hashes for excellxgene-2.8.8.tar.gz
Algorithm Hash digest
SHA256 9ac49492b0c381ac339a64bd32cf6e97294d810f55e3acea41faf434320183da
MD5 059b3e0b920ac4a911383ecd78d0ede5
BLAKE2b-256 faf6f864c4bf0a404585abcfc5aa8593c082daec940f751ef9b447d3929419db

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page