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Table 1 List of tools currently integrated/implemented in PIVOT

From: PIVOT: platform for interactive analysis and visualization of transcriptomics data

PIVOT Modules Tools Integrated
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
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