# broadSeq : for streamlined exploration of RNA-seq data

## Documentation for package ‘broadSeq’ version 1.5.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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.