Introduction | Feature Description | Installation | Functions | Methods | Model | The DeMixT algorithm for deconvolution | Examples | Simulated two-component data | Simulated three-component data | Real data: PRAD in TCGA dataset | Obtain raw read counts for the tumor and normal RNAseq data | Data preprocessing | Deconvolution using DeMixT | Deconvolution using normal reference samples from GTEx | Reference | Session Info
Package: DeMixT 2.0.0
Ruonan Li
DeMixT: Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms
DeMixT is a software package that performs deconvolution on transcriptome data from a mixture of two or three components.
Authors:
DeMixT_2.0.0.tar.gz
DeMixT_2.0.0.zip(r-4.7-x86_64)DeMixT_2.0.0.zip(r-4.6-x86_64)DeMixT_2.0.0.zip(r-4.5-x86_64)
DeMixT_2.0.0.tgz(r-4.6-x86_64)DeMixT_2.0.0.tgz(r-4.6-arm64)DeMixT_2.0.0.tgz(r-4.5-x86_64)DeMixT_2.0.0.tgz(r-4.5-arm64)
DeMixT_2.0.0.tar.gz(r-4.7-arm64)DeMixT_2.0.0.tar.gz(r-4.7-x86_64)DeMixT_2.0.0.tar.gz(r-4.6-arm64)DeMixT_2.0.0.tar.gz(r-4.6-x86_64)
DeMixT_2.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DeMixT/json (API)
| # Install 'DeMixT' in R: |
| install.packages('DeMixT', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- test.data.2comp - Simulated two-component test data
- test.data.3comp - Simulated three-component mixed cell line test data
On BioConductor:DeMixT-2.1.0(bioc 3.24)DeMixT-2.0.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwarestatisticalmethodclassificationgeneexpressionsequencingmicroarraytissuemicroarraycoveragecppopenmp
Last updated from:e3cf679db5 (on RELEASE_3_23). Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 214 | ||
| linux-devel-arm64 | NOTE | 330 | ||
| linux-devel-x86_64 | NOTE | 375 | ||
| source / vignettes | OK | 309 | ||
| linux-release-arm64 | NOTE | 326 | ||
| linux-release-x86_64 | NOTE | 358 | ||
| macos-release-arm64 | NOTE | 227 | ||
| macos-release-x86_64 | NOTE | 431 | ||
| macos-oldrel-arm64 | NOTE | 202 | ||
| macos-oldrel-x86_64 | NOTE | 496 | ||
| windows-devel | NOTE | 409 | ||
| windows-release | NOTE | 427 | ||
| windows-oldrel | NOTE | 463 | ||
| wasm-release | OK | 181 |
Exports:batch_correctionDeMixNBDeMixNB_preprocessingDeMixTDeMixT_DEDeMixT_GSDeMixT_preprocessingDeMixT_S2detect_suspicious_sample_by_hierarchical_clustering_2compgene_selection_DEOptimum_KernelCplot_dimplot_sdscale_normalization_75th_percentilesimulate_2compsimulate_3compsubset_sdsubset_sd_gene_remaining
Dependencies:abindannotateAnnotationDbiaskpassbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemclicodetoolscpp11crayoncurlDBIDelayedArraydendextendedgeRevdfarverfastmapfitdistrplusformatRfutile.loggerfutile.optionsgenefiltergenericsGenomicRangesggplot2glueGPArotationgridExtragtablehttrIRangesisobandjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixmatrixcalcMatrixGenericsmatrixStatsmemoisemgcvmimemnormtnlmeopensslpbapplypkgconfigpngpsychR6RColorBrewerRcpprlangRSQLiteS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystatmodSummarizedExperimentsurvivalsvasystruncdistvctrsviridisviridisLitewithrXMLxtableXVector
A Vignette for DeMixT
Last update: 2026-03-26
Started: 2026-03-26
DeMixNB: Deconvolution for Sparse Count Data
Introduction | Feature Description | Functions | Methods | Model | The DeMixNB Algorithm for Deconvolution | Real data Example | Spatially Resolved Transcriptomics | Results | Session Information
Last update: 2026-03-26
Started: 2026-03-26
