broadSeq : for streamlined exploration of RNA-seq data

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Documentation for package ‘broadSeq’ version 0.99.3

Help Pages

broadSeq-package broadSeq : for streamlined exploration of RNA-seq data
assay_plot Expression of multiple genes/features from a single assay as boxplot (or added dotplot)
biplotAnyPC Perform Principal Components Analysis
broadSeq broadSeq : for streamlined exploration of RNA-seq data
combinedEnrichment Provides GO gene set enrichment and over-representation analysis
genes_plot Expression of multiple genes/features from a single assay as boxplot (or added dotplot)
getFeatureLoadRanking Perform Principal Components Analysis
normalizeEdgerCPM Use of edgeR package to normalize count data
plotAnyPC Perform Principal Components Analysis
plotHeatmapCluster Plot clustered heatmaps
plot_MDS Classical multidimensional scaling
prcompTidy Perform Principal Components Analysis
round_df Applies round function only on numeric columns of a data.frame.
sampleAssay_plot Useful to visualize distribution of assay values for each sample. Plots 'boxplot' of any assay for each sample. Aesthetic can be added from colData.
transformDESeq2 Transform SummarizedExperiment with DESeq2 package
use_DELocal To use SummarizedExperiment with package DELocal
use_deseq2 To use SummarizedExperiment with package DESeq2
use_EBSeq To use SummarizedExperiment with package EBSeq
use_edgeR To use SummarizedExperiment with package edgeR
use_edgeR_exact To use SummarizedExperiment with package edgeR
use_edgeR_GLM To use SummarizedExperiment with package edgeR
use_limma To use SummarizedExperiment with package limma
use_limma_trend To use SummarizedExperiment with package limma
use_limma_voom To use SummarizedExperiment with package limma
use_multDE To identify differentially expressed genes by multiple methods
use_NOIseq Differential expression method for NOISeq
use_SAMseq To use SummarizedExperiment with package samr
volcanoPlot Volcano plot with formatted x and y axis label.