Introduction | Installation | Examples | Comparing between two species, human and chimpanzee as an example | Query ortholog information and estimate scaling factor | Create inputs for differentially expressed analysis and correlation estimation | Differentially expressed analysis (DE analysis) | Correlation analysis | Explore your result using appTEKRABber(): | Comparing control and treatment samples within the same species | DE analysis
Package: TEKRABber 1.17.0
Yao-Chung Chen
TEKRABber: An R package estimates the correlations of orthologs and transposable elements between two species
TEKRABber is made to provide a user-friendly pipeline for comparing orthologs and transposable elements (TEs) between two species. It considers the orthology confidence between two species from BioMart to normalize expression counts and detect differentially expressed orthologs/TEs. Then it provides one to one correlation analysis for desired orthologs and TEs. There is also an app function to have a first insight on the result. Users can prepare orthologs/TEs RNA-seq expression data by their own preference to run TEKRABber following the data structure mentioned in the vignettes.
Authors:
TEKRABber_1.17.0.tar.gz
TEKRABber_1.17.0.zip(r-4.7)TEKRABber_1.17.0.zip(r-4.6)TEKRABber_1.17.0.zip(r-4.5)
TEKRABber_1.17.0.tgz(r-4.6-x86_64)TEKRABber_1.17.0.tgz(r-4.6-arm64)TEKRABber_1.17.0.tgz(r-4.5-x86_64)TEKRABber_1.17.0.tgz(r-4.5-arm64)
TEKRABber_1.17.0.tar.gz(r-4.7-arm64)TEKRABber_1.17.0.tar.gz(r-4.7-x86_64)TEKRABber_1.17.0.tar.gz(r-4.6-arm64)TEKRABber_1.17.0.tar.gz(r-4.6-x86_64)
TEKRABber_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
TEKRABber/json (API)
| # Install 'TEKRABber' in R: |
| install.packages('TEKRABber', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ferygood/tekrabber/issues
Datasets:
- ctInputDE - Input expression data of gene/TE for differentially expressed analysis within same species
- fetchDataHmChimp - Example output comparing human and chimpanzee data using orhtologScale
- hg38_panTro6_rmsk - Repeatmasker track annotations with human and chimpanzee
- speciesCounts - Gene/TE expression data from human/chimpanzee brain RNA-seq
On BioConductor:TEKRABber-1.17.0(bioc 3.24)TEKRABber-1.16.0(bioc 3.23)
differentialexpressionnormalizationtranscriptiongeneexpressionbioconductorcpp
Last updated from:147c15f0de. Checks:1 WARNING, 11 ERROR, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 215 | ||
| linux-devel-arm64 | ERROR | 658 | ||
| linux-devel-x86_64 | ERROR | 718 | ||
| source / vignettes | OK | 347 | ||
| linux-release-arm64 | ERROR | 476 | ||
| linux-release-x86_64 | ERROR | 671 | ||
| macos-release-arm64 | ERROR | 382 | ||
| macos-release-x86_64 | ERROR | 1110 | ||
| macos-oldrel-arm64 | ERROR | 659 | ||
| macos-oldrel-x86_64 | ERROR | 1514 | ||
| windows-devel | ERROR | 810 | ||
| windows-release | ERROR | 822 | ||
| windows-oldrel | ERROR | 800 | ||
| wasm-release | OK | 222 |
Exports:appTEKRABbercorrOrthologTEDECorrInputsDEgeneTEorthologScaleprepareRMSK
Dependencies:abindAnnotationDbiAnnotationHubapeglmaskpassbbmlebdsmatrixBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbitbit64bitopsblobcachemcigarilloclicodacodetoolscpp11crayoncurlDBIdbplyrDelayedArrayDESeq2doParalleldplyremdbookfarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablehmshttrhttr2IRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimemvtnormnumDerivopensslpillarpkgconfigplyrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppNumericalRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSCBNSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrsviridisLitewithrXMLxml2XVectoryaml
