v3.1

• Added install_VIPlight.sh to improve installation speed and compatibility without CLI (Command Line Interface) modules
• Added CosMx spatial transcriptomics visualization capability

v3.0

• Upgraded to cellxgene v1.1.1
• Added specificity scores of cell types

v2.8

• More types of violin plot

v2.6

• Added visualization module of multiome data
• Improved spatial transcriptomics module

v2.5

• Added testing function from user interface
• Upgraded to cellxgene v0.16.7
• Using description file instead of description line in h5ad file

v2.4

• Using yml file to install python modules
• R in conda environment can be used

v2.2

• FIx a bug if rules of description line is not followed exactly

Add short description and initial graph settings. “|” and “by” are delimiters for VIP to parse the initial settings. Please follow the same rule for your own h5ad files. Please ensure to use matching names (umap, cell_type) in your data set.

adata.obs['>Description'] = ['Human brain snRNAseq 46k cells (MS Nature 2019 Schirmer et al.); data - normalized, log transformed and scaled UMI; platform - 10X v2 chemistry | embedding by umap; color by cell_type']*adata.n_obs

v2.1

• Specified versions of python modules in config.sh
• Works with multiple data sets under a root directory

v2.0

• Upgraded to cellxgene v0.16.4

v1.1.1

• minor improvement on installation
• created ver1.x branch that is based on cellxgene v0.15.0