This PR alters the single cell pipeline to address spike handling and normalisation associated with clustering (somewhat related issues). This comprises the following changes:
Use current versions of scater and SC3, removing downgrade operations in install script. This allows proper usage of SingleCellExperiment rather than legacy Scater object types.
Adds a library-size normalisation (using popular EBI single-cell method 'scran') between quantification and SC3. Genes and spikes (where applicable) have normalisation factors calculated separately. Option added for use of spike factors in normalisation, but since spike normalisation can be tricky this option is not used.
Both raw and normalised matrices used to construct the SingleCellExperiment object used by SC3. Spikes marked properly for SC3 such that they are not involved in clustering.
This PR alters the single cell pipeline to address spike handling and normalisation associated with clustering (somewhat related issues). This comprises the following changes:
Use current versions of scater and SC3, removing downgrade operations in install script. This allows proper usage of SingleCellExperiment rather than legacy Scater object types.
Adds a library-size normalisation (using popular EBI single-cell method 'scran') between quantification and SC3. Genes and spikes (where applicable) have normalisation factors calculated separately. Option added for use of spike factors in normalisation, but since spike normalisation can be tricky this option is not used.
Both raw and normalised matrices used to construct the SingleCellExperiment object used by SC3. Spikes marked properly for SC3 such that they are not involved in clustering.