Table 1 List of tools currently integrated/implemented in PIVOT

Normalization

DESeq, Modified DESeq, TMM, Upper quartile, CPM/RPKM/TPM, RUV, Spike-in regression, Census

Feature/Sample Filtering

List based, Expression based and Quality based filters

Basic Analysis Modules

Data distribution plots, Dispersion analysis, Rank-frequency plot, Spike-in analysis, Feature heatmap, etc.

Differential Expression

DESeq2, edgeR, SCDE, Monocle, Mann-Whitney U test

Clustering/Classification

Hierarchical, K-means, SC3, Community detection, Classification with caret, Cell state ordering with Monocle2/Diffusion pseudotime

Dimension Reduction

PCA, t-SNE, Metric/Non-Metric MDS, penalized LDA,

Diffusion Map

Correlation Analysis

Pairwise scatter plots, Sample/feature correlation heatmap,

Co-expression analysis

Gene Set Enrichment Analysis

KEGG pathway analysis, Gene ontology analysis

Network Analysis

STRING protein association network, Regnetwork visualization, Mogrify based trans-differentiation factor prediction

Other Utilities

Data map, Gene ID/Name conversion, BioMart gene annotation query, Venn diagram, Report generation, State saving