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Table 1 Comprehensive overview of NASQAR applications

From: NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization

  Analysis type Features / Functions Main R Packages Input Output Visualization
GeneCountMerger Preprocessing Merge counts files into a matrix format that is needed for many downstream analysis; also offers gene id/name conversion base R packages gene count files (Eg. output count files from htseq) csv file containing a matrix of samples and corresponding gene counts N/A
mergeFPKMs Preprocessing Merge sample fpkm files into a matrix format; also offers gene id/name conversion base R packages sample gene fpkm files (Eg. sample fpkm files from Cufflinks) csv file containing a matrix of samples and corresponding gene fpkm values N/A
Deseq2Shiny RNAseq (bulk) Differential Gene Expression (DGE) analysis and optionally Surrogate Variable Analysis (SVA) for hidden batch effect detection DESeq2, SVA matrix of samples and gene counts (csv) and optionally a metadata table (csv) VST matrix, Rlog matrix, DGE results table, Gene expression table, normalized counts matrix Distance heatmap, PCA plots, MA plots, Gene expression boxplots, normalized counts heatmap, SVA plots
START RNAseq (bulk) Differential Gene Expression (DGE) analysis edgeR, limma-voom matrix of samples and gene counts (csv) Gene expression table PCA plots, Heatmaps, Scatter plots, Volcano plots, Gene expression boxplots
DEApp RNAseq (bulk) Differential Gene Expression (DGE) analysis DESeq2, edgeR, limma-voom matrix of samples and gene counts (csv) and a metadata table (csv) DGE results table, method comparison results PCA plots, Dispersion plot, Volcano plot, Venn diagram method comparison
Seurat(V3)Wizard RNAseq (single-cell) Guided single-cell RNA-seq data analysis and clustering. Seurat, sctransform, dplyr either 10X data files (mtx, tsv) OR matrix of cell/gene counts PCA results, ICA results, DGE cluster markers table, Seurat R Object, R script Violin plots, PCA plots, PCA heatmaps, Elbow Plot,UMAP, t-SNE
Shaman Metagonomics Differential analysis of quantitative metagenomic data DESeq2, circlize, ape, phytools, philentropy a BIOM matrix file OR a counts file (csv)/taxonomy file (tsv). Optionally a phylogenetic tree newick file (nhx) and/or fastq files Output files (biom, tsv, nhx) of Shaman workflow that can be used in downstream metagenomic analysis and visualization within Shaman Bar plots, PCOA/PCA plots, Clustering dendograma, Rarefaction curves, Scatter plots, Heatmaps, Box plots, Diversity plots, Venn diagram
ClusterProfShinyGSEA Gene Enrichment - Gene Set Enrichment Analysis Gene Set Enrichment Analysis (GSEA) of GO-Terms and KEGG pathways clusterProfiler, DOSE, Goplot, enrichplot, pathview a table of differential gene expression DGE data (csv/tsv) GO terms table, KEGG results table Dot plots, Category netplot, GO induced graph, Pathview plot, ridge plot, pubmed trends
ClusterProfShinyORA Gene Enrichment - Over Respresentation Analysis Over-representation analysis of GO-Terms and KEGG pathways clusterProfiler, DOSE, Goplot, enrichplot, pathview, wordcloud2 a table of differential gene expression DGE data (csv/tsv) GO terms table, KEGG results table Bar plots, Dot plots, Category netplot, GO induced graph, Pathview plot, word cloud