Package: DegNorm 1.23.0

Ji-Ping Wang

DegNorm: DegNorm: degradation normalization for RNA-seq data

This package performs degradation normalization in bulk RNA-seq data to improve differential expression analysis accuracy. It provides estimates for each gene within each sample.

Authors:Ji-Ping Wang [aut, cre]

DegNorm_1.23.0.tar.gz
DegNorm_1.23.0.zip(r-4.7)DegNorm_1.23.0.zip(r-4.6)DegNorm_1.21.0.zip(r-4.5)
DegNorm_1.23.0.tgz(r-4.6-x86_64)DegNorm_1.23.0.tgz(r-4.6-arm64)DegNorm_1.21.0.tgz(r-4.5-x86_64)DegNorm_1.21.0.tgz(r-4.5-arm64)
DegNorm_1.23.0.tar.gz(r-4.7-arm64)DegNorm_1.23.0.tar.gz(r-4.7-x86_64)DegNorm_1.23.0.tar.gz(r-4.6-arm64)DegNorm_1.23.0.tar.gz(r-4.6-x86_64)
DegNorm_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DegNorm/json (API)

# Install 'DegNorm' in R:

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

Bug tracker:https://github.com/jipingw/degnorm/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

Datasets:

coverage_res_chr21 - Example CoverageClass data
res_DegNorm_chr21 - Example DegNormClass data

On BioConductor:DegNorm-1.23.0(bioc 3.24)DegNorm-1.22.0(bioc 3.23)

rnaseq normalization geneexpression alignment coverage differentialexpression batcheffect software sequencing immunooncology qualitycontrol dataimport openblas cpp openmp

5.38 score 2 stars 4 scripts 4 mentions 8 exports 152 dependencies

Last updated from:facd45b710. Checks:9 NOTE, 2 OK, 3 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	225
linux-devel-arm64	NOTE	414
linux-devel-x86_64	NOTE	541
source / vignettes	OK	478
linux-release-arm64	NOTE	425
linux-release-x86_64	NOTE	509
macos-release-arm64	NOTE	403
macos-release-x86_64	NOTE	614
macos-oldrel-arm64	FAIL	115
macos-oldrel-x86_64	FAIL	176
windows-devel	NOTE	465
windows-release	NOTE	444
windows-oldrel	FAIL	84
wasm-release	OK	238

Exports:degnorm plot_boxplot plot_corr plot_coverage plot_heatmap read_coverage_batch summary_CoverageClass summary_DegNormClass

Dependencies:abind AnnotationDbi askpass assertthat base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob bslib ca cachem callr cigarillo cli cluster codetools colorspace cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray dendextend digest doParallel dplyr egg evaluate farver fastmap filelock fontawesome foreach formatR fs futile.logger futile.options gclus generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable heatmaply highr hms htmltools htmlwidgets httr httr2 IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime nlme openssl otel permute pillar pkgconfig plotly plyr png prettyunits processx progress promises ps purrr qap R6 rappdirs RColorBrewer Rcpp RcppArmadillo RCurl registry reshape2 restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo seriation snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex TSP txdbmaker UCSC.utils utf8 vctrs vegan viridis viridisLite webshot withr xfun XML xml2 XVector yaml

DegNorm: an R package for degradation normalization for RNA-seq data

Rendered fromDegNorm.Rmdusingknitr::rmarkdown

Last update: 2022-06-03
Started: 2020-04-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
DegNorm: degradation normalization for RNA-seq data	DegNorm-package
Example CoverageClass data	coverage_res_chr21
Main function to perform degradation normalization.	degnorm
Degradation index (DI) score plot functions	plot_boxplot plot_corr plot_heatmap
Coverage plot functions for DegNorm	plot_coverage
Compute the read coverage score and read counts for all genes in batch mode	read_coverage_batch
Example DegNormClass data	res_DegNorm_chr21
Summary method for CoverageClass.	summary_CoverageClass
Summary method for DegNormClass.	summary_DegNormClass