Package: DeMixT 1.23.0

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:Zeya Wang <[email protected]>, Shaolong Cao<[email protected]>, Wenyi Wang <wwang7@@mdanderson.org>

DeMixT_1.23.0.tar.gz
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DeMixT.pdf |DeMixT.html✨
DeMixT/json (API)
NEWS

# Install 'DeMixT' in R:

install.packages('DeMixT', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

Datasets:

test.data.2comp - Simulated two-component test data
test.data.3comp - Simulated three-component mixed cell line test data

On BioConductor:DeMixT-1.23.0(bioc 3.21)DeMixT-1.22.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

software statisticalmethod classification geneexpression sequencing microarray tissuemicroarray coverage cpp openmp

5.27 score 25 scripts 235 downloads 5 mentions 15 exports 139 dependencies

Last updated 4 months agofrom:eb1e461c60. Checks:1 OK, 8 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 16 2025
R-4.5-win-x86_64	WARNING	Feb 16 2025
R-4.5-linux-x86_64	WARNING	Feb 16 2025
R-4.4-win-x86_64	WARNING	Feb 16 2025
R-4.4-mac-x86_64	WARNING	Feb 16 2025
R-4.4-mac-aarch64	WARNING	Feb 16 2025
R-4.3-win-x86_64	WARNING	Feb 16 2025
R-4.3-mac-x86_64	WARNING	Jan 17 2025
R-4.3-mac-aarch64	WARNING	Jan 17 2025

Exports:batch_correction DeMixT DeMixT_DE DeMixT_GS DeMixT_preprocessing DeMixT_S2 detect_suspicious_sample_by_hierarchical_clustering_2comp Optimum_KernelC plot_dim plot_sd scale_normalization_75th_percentile simulate_2comp simulate_3comp subset_sd subset_sd_gene_remaining

Dependencies:abind annotate AnnotationDbi askpass assorthead base64enc beachmat BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome bslib bsseq cachem cli codetools colorspace cpp11 crayon curl data.table DBI DelayedArray DelayedMatrixStats dendextend digest DSS edgeR evaluate evd fansi farver fastmap fontawesome formatR fs futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 glue GPArotation gridExtra gtable gtools h5mread HDF5Array highr htmltools httr IRanges isoband jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix matrixcalc MatrixGenerics matrixStats memoise mgcv mime mnormt munsell nlme openssl permute pillar pkgconfig plogr png psych R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sass scales snow SparseArray sparseMatrixStats statmod SummarizedExperiment survival sva sys tibble tinytex truncdist UCSC.utils utf8 vctrs viridis viridisLite withr xfun XML xtable XVector yaml

A Vignette for DeMixT

Rendered fromdemixt.Rmdusingknitr::rmarkdownon Feb 16 2025.

Last update: 2024-07-23
Started: 2019-02-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
batch_correction	batch_correction
Deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms	DeMixT
Estimates the proportions of mixed samples for each mixing component	DeMixT_DE
Estimates the proportions of mixed samples for each mixing component using profile likelihood gene selection	DeMixT_GS
DeMixT_preprocessing	DeMixT_preprocessing
Deconvolves expressions of each individual sample for unknown component	DeMixT_S2
detect_suspicious_sample_by_hierarchical_clustering_2comp	detect_suspicious_sample_by_hierarchical_clustering_2comp plot_dim plot_sd
Kernel function for optimizing parameters and hidden variables in DeMixT	Optimum_KernelC
scale_normalization_75th_percentile	scale_normalization_75th_percentile
Function to simulate two-component test data	simulate_2comp
Function to simulate three-component mixed cell line test data	simulate_3comp
subset_sd	subset_sd
subset_sd_gene_remaining	subset_sd_gene_remaining
Simulated two-component test data	test.data.2comp
Simulated three-component mixed cell line test data	test.data.3comp

Usage by other packages (reverse dependencies)