run_dea()
Run differential expression analysis
check_sample()
Check that targets file contains the necessary info in the right format
sanity_check()
Import the metadata and check it is correct
run_tximport()
Wrapper function to run tximport
run_fastqc()
QC reports for fastq files using FastQC
trim_fastq()
An R-based wrapper for Trim Galore!
run_multiqc()
Generate MultiQC report for FastQC
build_index()
Build index for mapping using Salmon
run_salmon()
Quantify transcript abundances using Salmon
deseq2_analysis()
Run DESeq2 analysis on RNA-seq count data
edger_analysis()
Run edgeR analysis on RNA-seq count data
limma_voom_analysis()
Run Limma-voom analysis on RNA-seq count data
exploratory_analysis_edger()
Exploratory analysis of edgeR data
exploratory_analysis_deseq2()
Exploratory analysis of DESeq2 data
make_heatmap()
Create heatmap with clustering of samples and genes for DEGs
make_MA()
Create MA plot
make_PCA()
Create PCA plot for transformed data
make_scree()
Create scree plot from prcomp data
make_upset()
Plot intersections of list of DE genes
make_volcano()
Create Volcano Plot
pathway_analysis()
Title
annotate_data()
Annotate gene data
read_salmon()
Read the run info from Salmon output