Package: ExpGenetic 0.1.0
ExpGenetic: Non-Additive Expression Analysis of Hybrid Offspring
Three functional modules, including genetic features, differential expression analysis and non-additive expression analysis were integrated into the package. And the package is suitable for RNA-seq and small RNA sequencing data. Besides, two methods of non-additive expression analysis were provided. One is the calculation of the additive (a) and dominant (d), the other is the evaluation of expression level dominance by comparing the total expression of the gene in hybrid offspring with the expression level in parents. For non-additive expression analysis of RNA-seq data, it is only applicable to hybrid offspring (including two sub-genomes) species for the time being.
Authors:
ExpGenetic_0.1.0.tar.gz
ExpGenetic_0.1.0.zip(r-4.5)ExpGenetic_0.1.0.zip(r-4.4)ExpGenetic_0.1.0.zip(r-4.3)
ExpGenetic_0.1.0.tgz(r-4.4-any)ExpGenetic_0.1.0.tgz(r-4.3-any)
ExpGenetic_0.1.0.tar.gz(r-4.5-noble)ExpGenetic_0.1.0.tar.gz(r-4.4-noble)
ExpGenetic_0.1.0.tgz(r-4.4-emscripten)ExpGenetic_0.1.0.tgz(r-4.3-emscripten)
ExpGenetic.pdf |ExpGenetic.html✨
ExpGenetic/json (API)
| # Install 'ExpGenetic' in R: |
| install.packages('ExpGenetic', repos = c('https://w123yu.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/w123yu/expgenetic/issues
- F1_miRNA_count - Count table of miRNAs in F1 (F1: the polyploid progeny).
- F1_miRNA_rpm - RPM table of miRNAs in F1 (F1: the polyploid progeny).
- F1_sRNA_seq - All sRNA sequences in F1 (F1: the polyploid progeny).
- P1_miRNA_count - Count table of miRNAs in P1 (P1: one of the parents).
- P1_miRNA_rpm - RPM table of miRNAs in P1 (P1: one of the parents).
- P1_sRNA_seq - All sRNA sequences in P1 (P1: one of the parents).
- P2_miRNA_count - Count table of miRNAs in P2 (P2: one of the parents).
- P2_miRNA_rpm - RPM table of miRNAs in P2 (P2: one of the parents).
- P2_sRNA_seq - All sRNA sequences in P2 (P2: one of the parents).
Last updated 2 years agofrom:dff9aefc0a. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 05 2024 |
| R-4.5-win | OK | Nov 05 2024 |
| R-4.5-linux | OK | Nov 05 2024 |
| R-4.4-win | OK | Nov 05 2024 |
| R-4.4-mac | OK | Nov 05 2024 |
| R-4.3-win | OK | Nov 05 2024 |
| R-4.3-mac | OK | Nov 05 2024 |
Exports:basepreplotCountfilterGet12BinsGetDAtableGetDEdatalenplotmirnapredatapolyDESeqRpmfiltersrnapredataVennDataVennPlot
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelclicodetoolscolorspacecpp11crayoncurlDelayedArrayDESeq2fansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggscigluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigplyrR6RColorBrewerRcppRcppArmadillorlangS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8vctrsVennDiagramviridisLitewithrXVectorzlibbioc
