scelvis 0.8.9

Single-cell RNA-seq data visualization

SCelVis: Easy Single-Cell Visualization

Documentation

The SCelVis documentation at ReadTheDocs.org contains comprehensive information including a Tutorial.

Movie

Installation

You can install with Pip and Bioconda or run directly via Docker.

$ pip install scelvis
# OR
$ conda install scelvis
# OR
$ docker run ghcr.io/bihealth/scelvis:0.8.8-0 scelvis --help

Look up the latest version (instead of 0.8.8-0 to use at here)

Building Docker Image

1. Push changes to Github (we need a [git tree-ish](https://stackoverflow.com/questions/4044368/what-does-tree-ish-mean-in-git), so a tag works as well as a feature branch).

2. Call GIT_TAG=tag-or-branch bash docker/build-docker.sh.

3. Run with docker run ghcr.io/bihealth/scelvis:[version]-0.

4. Push with docker push ghcr.io/bihealth/scelvis:[version]-0.

History

v0.8.9

• avoid loading datasets just to get meta-data

• update dash imports

v0.8.8

• fixing problem with categorical data:wq

v0.8.7

• fixing problem with ports in HTTP URLs

v0.8.6

• bug fixes for cell filtering

v0.8.5

• allow text import with mtx files

• display only most frequent categories

• use ad.raw if present

• enable downsampling during conversion

• link to publication

v0.8.4

• fix bug in custom static folder route

• fix iRODS authentication defaults

v0.8.3

• allow custom markdowns for home screen

• enable gene-gene plots and change colormap for gene scatter

v0.8.2

• fix iRODS authentication issues

• update docs for .h5ad input

v0.8.1

• fixing iframe sources (important if running behind reverse proxy with HTTPS)

• link documentation on home screen

v0.8.0

• adding sphinx documentation for ReadTheDocs

• upload and convert with IFrames; increase size limit

• add box plots

v0.7.3

• fix cache timeout error

v0.7.2

• fix ReferenceError

• updated README and tutorialmovie

v0.7.1

• improved cache handling

• improved user feedback for filtering & differential expression

v0.7.0

• added conversion from .loom files

• cell filtering also supports downsampling

• added PBMC dataset hosted on figshare

• added demo movie

v0.6.0

• cell filtering

• differential expression

v0.5.0

• upgrades to Dash v1

• fixes to UI, upload and conversion

• avoid creation of dense matrices

v0.4.1

• Fixing bug with specifying single .h5ad file as data source.

• Adding Dockerfile for building Docker images from intermediate versions.

v0.4.0

• Adding support for HTTP(S) data sources.

• Embedding about.md information in Anndata file.

• Adding support for passing

v0.3.0

• Adding example data set.

• Adding nice introduction to start page.

• Adding functionality for creating simple fake data set.

• Making import of ruamel_yaml more robust still.

• Adding tests.

• Adding Travis CI–based continuous integration tests.

v0.2.1

• Fixing SFTP support.

• Fixing import of ruamel_yaml.

v0.2.0

• More refactorization.

• Fixing dependency on ruamel-yaml to ruamel.yaml.

• Adding conversion feature.

• Adding upload feature.

• Adding support to load from SSHFS, FTP through pyfilesystem (no FTPS support).

• Adding support to load from iRODS, also works via tickets (pass ?ticket=TICKET to the query parameters).

v0.1.0

Initial release.

• Everything is new!