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)

V2.9.5

The latest stable version is V2.9.5. The current version of exCellxgene relies on anndata==0.7.8, so might crash with anndata objects generated with anndata==0.8.0 or above. Until we fix this bug, we recommend users to follow the installation instruction below. The key part is installing exCellxgene, then upgrading the anndata version to 0.8.0 in the "cxg" conda environment.

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
pip install anndata==0.8.0

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

Preprint on how to do manual cell-type annotation using interactive tools:

https://www.biorxiv.org/content/10.1101/2023.07.11.548639v1

Tutorial slides highligting some use cases:

https://cellxgene.cziscience.com/docs/05__Annotate%20and%20Analyze%20Your%20Data/5_8__Multimodal%20Annotations

More tutorial slides for multi-omics datasets (RNA, ATAC, CITE-seq, spatial transcriptomics) are coming soon (Q1/Q2 2024).

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

This version

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

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-2.9.5.tar.gz (7.3 MB view details)

Uploaded Source

File details

Details for the file excellxgene-2.9.5.tar.gz.

File metadata

  • Download URL: excellxgene-2.9.5.tar.gz
  • Upload date:
  • Size: 7.3 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.10.10

File hashes

Hashes for excellxgene-2.9.5.tar.gz
Algorithm Hash digest
SHA256 4afe175d93bc1134ce6d9d1542bf947c6bcdac83a7cc482b169f1eb7c728513c
MD5 64f29aa09bc3055367c939d36013d231
BLAKE2b-256 d133282c4604f1d66ee8e175b687e54b054fe259e3a45127bbe0c0ade30e943f

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