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
batchindicator 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
SeuratListobject 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 |