bioc-issue-bot
commented
4 months ago Hi @haibol2016
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: CleanUpRNAseq
Type: Package
Title: CleanUpRNAseq detects and corrects for genomic DNA contamination
in RNA-seq data
Version: 0.99.0
Authors@R: c(person("Haibo", "Liu",
role = c("aut", "cre"),
comment=c(ORCID="0000-0002-4213-2883"),
email = "haibo.liu@umassmed.edu"),
person("Kevin", "O'Connor", role = "ctb",
email = "Kevin.O'Connor@umassmed.edu"),
person("Michelle", "Kelliher", role = "ctb",
email = "Michelle.Kelliher@umassmed.edu"),
person("Lihua Julie", "Zhu", role = "aut",
email = "Julie.Zhu@umassmed.edu"),
person("Kai", "Hu", role = "aut",
email = "kai.hu@umassmed.edu"))
Description: 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.
biocViews: QualityControl, Sequencing, GeneExpression
License: GPL-3
Imports: ggplot2, plyranges, DESeq2, Rsamtools, Rsubread, pheatmap, reshape2,
GenomicRanges, edgeR, ensembldb, ggrepel, tximport, utils, magrittr,
grDevices, stats, graphics, Biostrings,SummarizedExperiment, methods,
devtools, BSgenome,qsmooth, AnnotationFilter, patchwork,
RColorBrewer, GenomeInfoDb, BiocGenerics, limma
Depends: R (>= 4.0.0)
Suggests: BiocManager, rmarkdown, RUnit, knitr, EnsDb.Hsapiens.v86, ggplotify,
BiocStyle, R.utils, AnnotationHub, BSgenome.Hsapiens.UCSC.hg38,
VignetteBuilder: knitr
RoxygenNote: 7.3.1
Roxygen: list(markdown = TRUE)
Encoding: UTF-8
LazyData: true
haibol2016
lshep
vjcitn
LiNk-NY
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