Package: InteRD 0.1.1
Chixiang Chen
InteRD: The Integrated and Robust Deconvolution
We developed the Integrated and Robust Deconvolution algorithm to infer cell-type proportions from target bulk RNA-seq data. This package is able to effectively integrate deconvolution results from multiple scRNA-seq datasets and calibrates estimates from reference-based deconvolution by taking into account extra biological information as priors. Moreover, the proposed algorithm is robust to inaccurate external information imposed in the deconvolution system.
Authors:
InteRD_0.1.1.tar.gz
InteRD_0.1.1.zip(r-4.5)InteRD_0.1.1.zip(r-4.4)InteRD_0.1.1.zip(r-4.3)
InteRD_0.1.1.tgz(r-4.4-any)InteRD_0.1.1.tgz(r-4.3-any)
InteRD_0.1.1.tar.gz(r-4.5-noble)InteRD_0.1.1.tar.gz(r-4.4-noble)
InteRD_0.1.1.tgz(r-4.4-emscripten)InteRD_0.1.1.tgz(r-4.3-emscripten)
InteRD.pdf |InteRD.html✨
InteRD/json (API)
NEWS
| # Install 'InteRD' in R: |
| install.packages('InteRD', repos = c('https://chencxxy28.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/chencxxy28/interd/issues
Last updated 2 years agofrom:335984b6b8. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 14 2024 |
| R-4.5-win | OK | Nov 14 2024 |
| R-4.5-linux | OK | Nov 14 2024 |
| R-4.4-win | OK | Nov 14 2024 |
| R-4.4-mac | OK | Nov 14 2024 |
| R-4.3-win | OK | Nov 14 2024 |
| R-4.3-mac | OK | Nov 14 2024 |
Exports:evaluategenerateBulkInteRD.predict.propInteRD1InteRD2pop.ct.prop.scRNARef_free
Dependencies:askpassBiobaseBiocGenericsbitbit64bootcellrangerclassclicliprcolorspacecowplotcpp11crayoncurldata.tableDescToolse1071Exactexpmfansifarverforcatsgenericsggplot2gldgluegtablehavenhmshttrisobandjsonlitelabelinglatticelifecyclelimSolvelmomlpSolvemagrittrMASSMatrixmgcvmimemunsellmvtnormnlmeopensslpheatmappillarpkgconfigplyrprettyunitsprogressproxyquadprogR6RColorBrewerRcppreadrreadxlrematchreshape2rlangrootSolverstudioapiscalesstringistringrsystibbletidyselecttzdbutf8vctrsviridisLitevroomwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Evaluation for estimated cell type proportions | evaluate |
| Pseudo bulk data generation function | generateBulk |
| Extract the estimated proportions from InteRD | InteRD.predict.prop |
| The InteRD1 estimate from reference ensemble | InteRD1 |
| The InteRD2 estimate | InteRD2 |
| Calculate the population-level cell type proportions from a single-cell data. | pop.ct.prop.scRNA |
| A reference-free deconvolution estimate | Ref_free |