Package: debCAM 1.25.0

Lulu Chen

debCAM: Deconvolution by Convex Analysis of Mixtures

An R package for fully unsupervised deconvolution of complex tissues. It provides basic functions to perform unsupervised deconvolution on mixture expression profiles by Convex Analysis of Mixtures (CAM) and some auxiliary functions to help understand the subpopulation-specific results. It also implements functions to perform supervised deconvolution based on prior knowledge of molecular markers, S matrix or A matrix. Combining molecular markers from CAM and from prior knowledge can achieve semi-supervised deconvolution of mixtures.

Authors:Lulu Chen <[email protected]>

debCAM_1.25.0.tar.gz
debCAM_1.25.0.zip(r-4.5)debCAM_1.25.0.zip(r-4.4)debCAM_1.25.0.zip(r-4.3)
debCAM_1.25.0.tgz(r-4.4-any)debCAM_1.25.0.tgz(r-4.3-any)
debCAM_1.25.0.tar.gz(r-4.5-noble)debCAM_1.25.0.tar.gz(r-4.4-noble)
debCAM_1.25.0.tgz(r-4.4-emscripten)debCAM_1.25.0.tgz(r-4.3-emscripten)
debCAM.pdf |debCAM.html✨
debCAM/json (API)
NEWS

# Install 'debCAM' in R:
install.packages('debCAM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/lululuella/debcam/issues

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT
Datasets:
  • ratMix3 - Gene expression data downsampled from GSE19380

On BioConductor:debCAM-1.25.0(bioc 3.21)debCAM-1.24.0(bioc 3.20)

softwarecellbiologygeneexpressionopenjdk

5.69 score 7 stars 14 scripts 272 downloads 18 exports 107 dependencies

Last updated 3 months agofrom:f694119745. Checks:7 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 13 2025
R-4.5-winOKJan 13 2025
R-4.5-linuxOKJan 13 2025
R-4.4-winOKJan 13 2025
R-4.4-macOKJan 13 2025
R-4.3-winOKJan 13 2025
R-4.3-macOKJan 13 2025

Exports:AfromMarkersAmatCAMCAMASestCAMMGClusterCAMPrepcornerSortMDLMGsforAMGstatisticPCAmatplotredoASestreselectMGsffsHullsimplexplotSmatXWProj

Dependencies:abindapclusteraskpassBHBiobaseBiocGenericsBiocManagerBiocParallelbitbit64classclicliprclustercodetoolscolorspacecorpcorcpp11crayoncurlDBIDelayedArraydigestDMwR2doParalleldplyrfansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgeometryggplot2gluegridBasegtablehmshttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclelinproglpSolvemagicmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellmvtnormnlmeNMFnnlsopensslpcaPPpillarpkgconfigplyrprettyunitsprogressquantmodR6RColorBrewerRcppRcppProgressreadrregistryreshape2rJavarlangrngtoolsrpartS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyselectTTRtzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxtsXVectorzoo

debCAM User Manual

Lulu Chen

Rendered fromdebcam.Rmdusingknitr::rmarkdownon Jan 13 2025.

Last update: 2019-10-24
Started: 2019-10-24