Components¶
We are building components in the following categories:
- Wrappers script packages for common single-cell analysis toolkits
- Bioconda packages to facilitate wrapper availability
- Bioconda packages for any previously missing packages
- Containers for Bioconda packages (mostly created automatically via Bioconda)
- Galaxy wrappers for Bioconda-packages wrappers
This page details components developed as part of this project..
Wrapper script packages¶
- workflowscriptscommon - Common functions for re-use over R package wrappers
- bioconductor-singlecellexperiment-scripts - Wrapper scripts around SingleCellExperiment R functions
- bioconductor-scater-scripts - Wrapper scripts around Scater R functions
- bioconductor-sc3-scripts - Wrapper scripts around SC3 R functions
- r-seurat-scripts - Wrapper scripts around Seurat R functions
- scanpy-scripts - Wrapper scripts for Scanpy functions
Bioconda packages¶
The above packages have been made available via Bioconda in the packages:
Containers¶
Use of Bioconda packages means we get containers ‘for free’ as well. See containers for:
- r-workflowscriptscommon
- bioconductor-singlecellexperiment-scripts
- bioconductor-scater-scripts
- bioconductor-sc3-scripts
- r-seurat-scripts
- scanpy-scripts
We have also developed the following:
- container-galaxy-sc-tertiary - Galaxy container for single cell RNA-Seq tertiary analysis tools
Galaxy components¶
Ongoing work¶
Recent updates in Bioconda provide access to newer versions of Bioconductor packages. In particular we’re aware that our Scater wrappers are currently out of date, for example the function for reading 10X data is removed in favour of DropletUtils. Updates will be applied in due course.