# Detect and Correct Genomic DNA Contamination in RNA-seq Data

## Documentation for package ‘CleanUpRNAseq’ version 1.2.0

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

## Help Pages

calc_gene_gc | Calculate GC content of genes
calc_region_gc | Calculate GC content of genomic regions
correct_GC | Correct DNA contamination considering GC-bias effect
correct_global | Global correction for DNA contamination
correct_IR | Correct gene expression using a linear model
correct_stranded | Correct for gDNA contamination in stranded libraries
create_summarizedcounts | Create an object of SummarizedCounts
feature_counts_list | GC content and lengths of 2000 intergenic regions
gene_GC | GC content and lengths of 2000 human genes
get_region_stat | Calculate read distribution over different types of genomic features
get_saf | Generate a SAF file for genomic features
intergenic_GC | GC content and lengths of 2000 intergenic regions
plot_assignment_stat | Visualize assignment statistics of reads/fragments by featureCounts
plot_expr_distr | Visualize expression distribution
plot_gene_content | Check the percentage of genes with counts greater than minimal CPM
plot_pca_heatmap | Check sample similarity and variation
plot_read_distr | Visualize read distribution among different genomic regions
plot_sample_corr | Visualize sample correlation
salmon_quant | GC content and lengths of 2000 intergenic regions
salmon_tximport | Import Salmon quantification output into R
style_BSgenome | Convert a BSgenome from the UCSC to the Ensembl style
SummarizedCounts | SummarizedCounts Object
summarize_reads | Summarize reads for different genomic features