What is DegNorm? | DegNorm pipline available formats | DegNorm version 1.3.4 updates | Install DegNorm R package | DegNorm main features | 1. Compute coverage score based on alignment .bam files | Set up input file: .bam and .gtf files. | Run main function to create read coverage matrix and read counts | 2. DegNorm core algorithm | 3. Plot functions in DegNorm | -- Plot the before-/after-degradation coverage curves | -- Boxplot of the degradation index(DI) scores | -- Heatmap plot of the degradation index(DI) scores | -- Correlation matrix plot of degradation index(DI) scores | Session info
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:
DegNorm_1.23.0.tar.gz
DegNorm_1.23.0.zip(r-4.7-x86_64)DegNorm_1.23.0.zip(r-4.7-arm64)DegNorm_1.23.0.zip(r-4.6-x86_64)DegNorm_1.23.0.zip(r-4.6-arm64)
DegNorm_1.23.0.tgz(r-4.6-x86_64)DegNorm_1.23.0.tgz(r-4.6-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:
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)
rnaseqnormalizationgeneexpressionalignmentcoveragedifferentialexpressionbatcheffectsoftwaresequencingimmunooncologyqualitycontroldataimportopenblascppopenmp
Last updated from:facd45b710. Checks:11 NOTE, 2 OK, 3 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 197 | ||
| linux-devel-arm64 | NOTE | 336 | ||
| linux-devel-x86_64 | NOTE | 394 | ||
| source / vignettes | OK | 469 | ||
| linux-release-arm64 | NOTE | 323 | ||
| linux-release-x86_64 | NOTE | 432 | ||
| macos-release-arm64 | NOTE | 276 | ||
| macos-release-x86_64 | NOTE | 636 | ||
| macos-oldrel-arm64 | FAIL | 99 | ||
| macos-oldrel-x86_64 | FAIL | 250 | ||
| windows-devel-arm64 | NOTE | 412 | ||
| windows-devel-x86_64 | NOTE | 419 | ||
| windows-release-arm64 | NOTE | 414 | ||
| windows-release-x86_64 | NOTE | 395 | ||
| windows-oldrel-x86_64 | FAIL | 103 | ||
| wasm-release | OK | 164 |
Exports:degnormplot_boxplotplot_corrplot_coverageplot_heatmapread_coverage_batchsummary_CoverageClasssummary_DegNormClass
Dependencies:AnnotationDbiaskpassassertthatbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibcacachemcallrcigarillocliclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrdendextenddigestdoParalleldplyreggevaluatefarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgclusgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragtableheatmaplyhighrhmshtmltoolshtmlwidgetshttrhttr2IRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlazyevallifecyclemagrittrMASSmemoisemimeopensslotelpillarpkgconfigplotlyplyrpngprettyunitsprocessxprogresspromisespspurrrqapR6rappdirsRColorBrewerRcppRcppArmadilloRCurlregistryreshape2restfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4VectorsS7sassscalesSeqinfoseriationsnowstringistringrsystibbletidyrtidyselecttinytexTSPtxdbmakerUCSC.utilsutf8vctrsviridisviridisLitewebshotwithrxfunXMLxml2XVectoryaml
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 |