ensemblemerge

Examples

Task	Colab	Jupyter	Version(Tag)
scRNA-seq normalization			v2.1.24-001
Reference-based scRNA-seq integration			v2.1.24-001
de novo scRNA-seq integration			v2.1.24-001

Preprocessing

• cell and gene filtering
• Check the integrity of the input data. For example, if a batch indicator is specified, it will validate whether the meta data is available.
• No batch related operations

Class	Method	Ref.
SeuratPreprocess

Normalization

Class	Method	Ref.
SCTransformNormalize	SCTransform	[Paper]
SeuratNormalize	Seurat's default normalization pipeline	[Paper]

Doublet detection

• The detected doublets are removed.
• If a SeuratList object is provided, the doublet detection is performed on each batch separately.

Class	Method	Ref.
scDblFinderDoubletDetect	scDblFinder	[Paper]
DoubletFinderDoubletDetect	DoubletFinder	[Paper]
ScrubletDoubletDetect	Scrublet	[Wolock et al. 2019]

Ambient RNA removal

• The adjusted counts will be used to replace the raw counts.

Class	Method	Ref.
decontXRemoveAmbientRNA	celda	[Yang et al. 2020]
soupXRemoveAmbientRNA	SoupX	[Young et al. 2020]

De novo integration

Class	Method	Ref.
SeuratMerge	Seurat(v3)
HarmonyMerge	Harmony	[Paper]
FastMNNMerge	FastMNN	[Paper]
LigerMerge	LIGER	[Paper]
BBKNNMerge
ScanoramaMerge
scVIMerge