Detect and Correct Genomic DNA Contamination in RNA-seq Data

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Documentation for package ‘CleanUpRNAseq’ version 1.0.0

• 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