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

Navigation

Verified details

These details have been verified by PyPI
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

Unverified details

These details have not been verified by PyPI
Project links
Meta
Classifiers

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

Verified details

These details have been verified by PyPI
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

Unverified details

These details have not been verified by PyPI
Project links
Meta
Classifiers

Release history Release notifications | RSS feed

2.9.6

2.9.5

2.9.4 yanked

2.9.2

2.9.1

2.9.0

2.8.11

2.8.10

2.8.9

2.8.8

2.8.7 yanked

Reason this release was yanked:

broken

2.8.6

2.8.5 yanked

Reason this release was yanked:

unstable

2.8.4 yanked

Reason this release was yanked:

unstable

2.8.3 yanked

Reason this release was yanked:

unstable

2.8.2 yanked

Reason this release was yanked:

unstable

2.8.1 yanked

Reason this release was yanked:

unstable

2.8.0 yanked

Reason this release was yanked:

unstable

2.7.6

2.7.5

2.7.4

2.7.3

2.7.2

2.7.1

2.7.0 yanked

Reason this release was yanked:

memory leakage with ray
This version

2.6.5

2.6.4

2.6.3

2.6.2

2.6.1

2.6.0 yanked

Reason this release was yanked:

premature release

2.5.6

2.5.5

2.5.4

2.5.3 yanked

Reason this release was yanked:

width of volcanoplot bugged

2.5.2

2.5.1

2.5.0

2.4.9

2.4.8

2.4.7

2.4.6 yanked

Reason this release was yanked:

Many things broken

2.4.5

2.4.4

2.4.3

2.4.2

2.4.1 yanked

Reason this release was yanked:

bug

2.4.0 yanked

Reason this release was yanked:

improperly-managed data types

2.3.9

2.3.8

2.3.7 yanked

Reason this release was yanked:

Sankey broken again

2.3.6

2.3.5

2.3.4 yanked

Reason this release was yanked:

Bug with scatter plots

2.3.3 yanked

Reason this release was yanked:

Windows pathing bug still present

2.3.2

2.3.0

2.2.9

2.2.8

2.2.7

2.2.6

2.2.4

2.2.3

2.2.2

2.2.1

2.2.0

2.1.9

2.1.8

2.1.7

2.1.6

2.1.5

2.1.4

2.1.3

2.1.2

2.1.1

2.1.0

2.0.5

2.0.4

2.0.3

2.0.2

2.0.1

2.0.0

1.3.5

1.3.4

1.3.3

1.3.2

1.3.1

1.3.0

1.2.18

1.2.17

1.2.16

1.2.15

1.2.14

1.2.13

1.2.12

1.2.11

1.2.10

1.2.9

1.2.8

1.2.7

1.2.5

1.2.4

1.2.3

1.2.2

1.2.1

1.2.0

1.1.11

1.1.10

1.1.9

1.1.8

1.1.7

1.1.6

1.1.5

1.1.4

1.1.3

1.1.2

1.1.1

1.1.0

1.0.9

1.0.8

1.0.7

1.0.6

1.0.5

1.0.4

1.0.3

1.0.2

1.0.1

1.0.0

Download files

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

Source Distribution

excellxgene-2.6.5.tar.gz (7.0 MB view details)

Uploaded Source

File details

Details for the file excellxgene-2.6.5.tar.gz.

File metadata

  • Download URL: excellxgene-2.6.5.tar.gz
  • Upload date:
  • Size: 7.0 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-2.6.5.tar.gz
Algorithm Hash digest
SHA256 c4658b52201fd876ffcb405aebf88a901abc9c9d10e0ea5fc4a81b989d6b5b4e
MD5 0fbf5142f70f160073027a1c225751f4
BLAKE2b-256 eda7077fdf576ed64f144136aca6e2e21934a3e1535ec14a1896158b284ef64f

See more details on using hashes here.

Provenance

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