parseR/NAMESPACE at master · anilchalisey/parseR · GitHub

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# Generated by roxygen2: do not edit by hand

export(aggregate_fqc)
export(align_rna)
export(count_reads)
export(create_contrast)
export(create_design)
export(create_fqreport)
export(create_hmp)
export(create_maplot)
export(create_mds)
export(create_pca)
export(create_se)
export(deseq2_norm)
export(deseq2_pipe)
export(edger_norm)
export(edger_pipe)
export(homer_denovo)
export(homer_known)
export(limma_pipe)
export(load_samples)
export(make_bigwig)
export(make_venn)
export(module_fqc)
export(plot_fqc)
export(process_counts)
export(read_fastqc)
export(read_multifastqc)
export(run_deseq2)
export(run_diff)
export(run_edger)
export(run_fastqc)
export(run_goseq)
export(run_goseqmsigdb)
export(run_hisat2)
export(run_homer)
export(run_limma)
export(run_sambambadup)
export(run_samflagstat)
export(run_samindex)
export(run_samsort)
export(run_samview)
export(stats_fqc)
import(ComplexHeatmap)
import(DESeq2)
import(SummarizedExperiment)
import(dplyr)
import(edgeR)
import(ggplot2)
import(ggthemes)
import(grid)
import(tools)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,counts)
importFrom(DESeq2,estimateSizeFactors)
importFrom(DESeq2,plotDispEsts)
importFrom(DESeq2,plotPCA)
importFrom(DESeq2,results)
importFrom(DESeq2,rlog)
importFrom(GenomicAlignments,coverage)
importFrom(GenomicAlignments,readGAlignmentPairs)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,idxstatsBam)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,metadata)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(data.table,fread)
importFrom(data.table,fwrite)
importFrom(edgeR,DGEList)
importFrom(edgeR,cpm)
importFrom(edgeR,decideTestsDGE)
importFrom(limma,contrasts.fit)
importFrom(limma,decideTests)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,makeContrasts)
importFrom(limma,plotMD)
importFrom(limma,plotMDS)
importFrom(limma,topTable)
importFrom(limma,voomWithQualityWeights)
importFrom(reshape2,melt)
importFrom(rmarkdown,render)
importFrom(rtracklayer,export.bw)
importFrom(stats,aggregate)
importFrom(tidyr,spread)