Asc-Seurat: analytical single-cell Seurat-based web application

BMC Bioinformatics

Table 1 Comparison of Asc-Seurat's capabilities with the most relevant web applications currently available

	Asc-Seurat	NASQR [11]	SCiAp [13]	PIVOT [8]	SC1 [14]	Stream [9]	alona [12]	ASAP [7]	BingleSeq [10]
Usability
Is it a web application?	Yes	Yes	Yes (2)	Yes	Yes	Yes	Yes	Yes	Yes
Easy to install (Docker)?	Yes	Yes	No	Yes	No	Yes	No	No	No
Easy to use by wet-lab biologists?	Yes	Yes	Yes (3)	Yes	Yes	Yes	Yes	Yes	Yes
Clustering
Does the clustering?	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes
Does the clustering using Seurat?	Yes	Yes	Yes	No	No	No	Yes	Yes	Yes
Is it capable of integrating multiple samples?	Yes	Yes (1)	NA	Yes	Yes (7)	No	No	NA	No
Offers the SCtransform normalization?	Yes	Yes	No	No	No	No	No	No	No
Allows the filtering of clusters of interest?	Yes	No	Yes (4)	No	NA	No	No	No	No
High-quality plots of the clustering and expression?	Yes	Yes	Yes	Yes (6)	Yes	No	Yes	Yes	Yes
Trajectory inference
Performs trajectory inference (TI)?	Yes	No	Yes	Yes	Yes	Yes	No	No	No
Offers multiple models for TI?	Yes	No	Yes	No	No	No	No	No	No
Differential Expression analysis within the trajectory?	Yes	No	Yes	Yes	No	Yes	No	No	No
Expression visualization within the trajectory?	Yes	No	Yes	Yes	No	Yes	No	No	No
Annotation
Gene annotation?	Yes	Yes	Yes (5)	Yes	Yes	No	No	Yes	Yes (8)
GO terms enrichment	Yes	Yes	Yes (5)	Yes	Yes	No	No	Yes	No

NA (not available): the authors could not address this question with the information available in the manual, tutorials, or publications related to the web application. 1—It is not clear how the integration is performed, but it appears not to use Seurat's integration approach. 2—It is based on the Galaxy framework. 3—Requires training in the Galaxy framework. 4—Users need to provide the cell IDs manually for exclusion. 5—It is possible when using other Galaxy modules. 6—Does not provide UMAP, which has become the most used visualization method for scRNA-seq clustered data. 7—It is capable of analyzing multiple samples. However, it seems not to apply Seurat's integration approach. 8—Available only for a limited set of model organisms

ISSN: 1471-2105