This pull request contains various major upgrades for BENGAL.
Maintainer: Yuyao Song ysong@ebi.ac.uk
Containerize: provide containers for homology mapping and integration steps.
Packages update: we now base the pipeline on the latest version of anndata: 0.9.2. We also updated all packages for integration algorithms to the latest in the containers and conda envs.
Conversion between anndata and Seurat objects: we now use sceasy for the conversion instead of SeuratDisk, which allows it to be an integrated part of the pipeline.
This pull request contains various major upgrades for BENGAL. Maintainer: Yuyao Song ysong@ebi.ac.uk
Containerize: provide containers for homology mapping and integration steps.
Packages update: we now base the pipeline on the latest version of anndata: 0.9.2. We also updated all packages for integration algorithms to the latest in the containers and conda envs.
Conversion between anndata and Seurat objects: we now use sceasy for the conversion instead of SeuratDisk, which allows it to be an integrated part of the pipeline.
Nextflow: prettify nextflow scripts and configs.
License: BENGAL now uses the GPLv3 license.