Man pages for HuntsmanCancerInstitute/hciR
RNA-seq workflows at HCI

annotate_resultsAnnotate DESeq2 results
as_matrixConvert tibbles to a matrix
check_contrastsCheck contrasts
deseq_from_tibbleRun DESeq from tibbles
extract_samplesParse sample from file names
fgsea_allRun fgsea on all DESeq2 result tables
filter_countsFilter count matrix
filter_top_countsFilter top count matrix
fisher_allRun Fisher's test on all DESeq2 result tables
fisher_barplotGene set enrichment using Fisher's test
gage_allRun GAGE on all DESeq2 result tables
gdc_coldataGDC column data
gdc_rowdataGDC row data
gene_intersectCompare genes to sets
palette255Expand RColorBrewer palettes
pasillaDESeq objects and results for Pasilla knock-downs
plot_biotypesPlot reads assigned to biotypes
plot_countsPlot counts for a single gene
plot_distPlot heatmap of sample distances
plot_fgseaPlot fGSEA output
plot_filterPlot count matrix to check filter cutoff
plot_gagePlot gage_all output
plot_genesPlot heatmap of top genes
plot_gseaPlot GSEA output
plot_interactionsPlot counts for many genes
plot_maHighchart version of MA-plot
plot_pcaHighchart version of plotPCA in DESeq2
plot_volcanoVolcano plot
read_biomartRead biomart annotations
read_featureCountsRead featureCounts output files
read_gseaRead GSEA enrichment files
read_idxstatsRead samtools idxstats output
read_RnaSeqMetricsRead CollectRnaSeqMetrics output
read_RSEMRead RSEM output files
read_sample_filesRead and combine common output files
read_STARRead STAR log files
reexportsObjects exported from other packages
results2Extract and annotate a single DESeq results table
results_allExtract and annotate all results from a DESeq analysis
r_logRegularized log transformation
sort_countsSort columns of a count matrix by rows in sample data
sort_samplesSort sample names
summary_DESeqSummarize DESeq2 results
summary_tibbleSummarize tibble columns
top_countsGet a count matrix of top genes
top_genesGet top genes
write_deseqWrite DESeq results
write_gsea_rnkWrite DESeq results to GSEA rank file
HuntsmanCancerInstitute/hciR documentation built on Nov. 6, 2019, 12:11 p.m.