Package: CleanUpRNAseq 1.1.1

Haibo Liu

CleanUpRNAseq: Detect and Correct Genomic DNA Contamination in RNA-seq Data

RNA-seq data generated by some library preparation methods, such as rRNA-depletion-based method and the SMART-seq method, might be contaminated by genomic DNA (gDNA), if DNase I disgestion is not performed properly during RNA preparation. CleanUpRNAseq is developed to check if RNA-seq data is suffered from gDNA contamination. If so, it can perform correction for gDNA contamination and reduce false discovery rate of differentially expressed genes.

Authors:Haibo Liu [aut, cre], Kevin O'Connor [ctb], Michelle Kelliher [ctb], Lihua Julie Zhu [aut], Kai Hu [aut]

CleanUpRNAseq_1.1.1.tar.gz
CleanUpRNAseq_1.1.1.zip(r-4.5)CleanUpRNAseq_1.1.1.zip(r-4.4)CleanUpRNAseq_0.99.15.zip(r-4.3)
CleanUpRNAseq_1.1.1.tgz(r-4.4-any)CleanUpRNAseq_0.99.15.tgz(r-4.3-any)
CleanUpRNAseq_1.1.1.tar.gz(r-4.5-noble)CleanUpRNAseq_1.1.1.tar.gz(r-4.4-noble)
CleanUpRNAseq_1.1.1.tgz(r-4.4-emscripten)CleanUpRNAseq_0.99.15.tgz(r-4.3-emscripten)
CleanUpRNAseq.pdf |CleanUpRNAseq.html✨
CleanUpRNAseq/json (API)
NEWS

# Install 'CleanUpRNAseq' in R:

install.packages('CleanUpRNAseq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/haibol2016/cleanuprnaseq/issues

Datasets:

feature_counts_list - GC content and lengths of 2000 intergenic regions
gene_GC - GC content and lengths of 2000 human genes
intergenic_GC - GC content and lengths of 2000 intergenic regions
salmon_quant - GC content and lengths of 2000 intergenic regions

On BioConductor:CleanUpRNAseq-1.1.0(bioc 3.21)CleanUpRNAseq-1.0.0(bioc 3.20)

qualitycontrol sequencing geneexpression

5.44 score 5 stars 4 scripts 124 downloads 19 exports 144 dependencies

Last updated 1 months agofrom:dac4dc8f69. Checks:OK: 4 NOTE: 2 ERROR: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 20 2024
R-4.5-win	NOTE	Nov 20 2024
R-4.5-linux	NOTE	Nov 20 2024
R-4.4-win	OK	Nov 20 2024
R-4.4-mac	OK	Nov 20 2024
R-4.3-win	ERROR	Sep 21 2024
R-4.3-mac	OK	Sep 21 2024

Exports:calc_gene_gc calc_region_gc correct_GC correct_global correct_IR correct_stranded create_summarizedcounts get_region_stat get_saf plot_assignment_stat plot_expr_distr plot_gene_content plot_pca_heatmap plot_read_distr plot_sample_corr salmon_tximport style_BSgenome summarize_reads SummarizedCounts

Dependencies:abind annotate AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome bslib cachem checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI DelayedArray DESeq2 digest edgeR ensembldb evaluate fansi farver fastmap fontawesome foreign formatR Formula fs futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggrepel glue gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl pheatmap pillar pkgconfig plogr plyr png ProtGenerics qsmooth R6 rappdirs RColorBrewer Rcpp RcppArmadillo RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi Rsubread rtracklayer S4Arrays S4Vectors sass scales snow SparseArray statmod stringi stringr SummarizedExperiment survival sva sys tibble tinytex tximport UCSC.utils utf8 vctrs viridis viridisLite withr xfun XML xtable XVector yaml zlibbioc

CleanUpRNAseq: detecting and correcting gDNA contamination in RNA-seq data

Haibo Liu, Kai Hu, Kevin O'Connor, Michelle Kelliher, Lihua Julie Zhu

Rendered fromCleanUpRNAseq.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2024-11-19
Started: 2024-05-08

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

Package: CleanUpRNAseq 1.1.1

CleanUpRNAseq: Detect and Correct Genomic DNA Contamination in RNA-seq Data

CleanUpRNAseq: detecting and correcting gDNA contamination in RNA-seq data

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Help Manual

Usage by other packages (reverse dependencies)