Package: seAMLess 0.1.2

E Onur Karakaslar

seAMLess: A Single Cell Transcriptomics Based Deconvolution Pipeline for Leukemia

Given a bulk transcriptomic (RNA-seq) sample of an Myeloid Leukemia patient calculates immune composition and drug resistance for different small-molecule inhibitors. Published in <https://www.nature.com/articles/s41698-024-00596-9>.

Authors:E Onur Karakaslar [aut, cre], Redmar van den Berg [ctb]

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seAMLess.pdf |seAMLess.html✨
seAMLess/json (API)

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

Bug tracker:https://github.com/eonurk/seamless/issues

Datasets:
  • exampleTCGA - TCGA-LAML bulk RNA-seq data downloaded from GDC
  • exampleTCGAmeta - TCGA-LAML example data meta file downloaded from GDC
  • grch38 - Grch38
  • minRes - A minimal seAMLess result list object
  • venoModel - Trained RF model on Venetoclax Resistance

On CRAN:

amldeconvolutionvenetoclax

3.60 score 2 stars 7 scripts 609 downloads 5 exports 34 dependencies

Last updated 2 months agofrom:8d4df9881c. Checks:1 OK, 7 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 17 2025
R-4.5-winWARNINGFeb 17 2025
R-4.5-macWARNINGFeb 17 2025
R-4.5-linuxWARNINGFeb 17 2025
R-4.4-winWARNINGFeb 17 2025
R-4.4-macWARNINGFeb 17 2025
R-4.3-winWARNINGFeb 17 2025
R-4.3-macWARNINGFeb 17 2025

Exports:cliseAMLessternaryPlotverboseFnwrangleMat

Dependencies:BiobaseBiocGenericsclicolorspacedata.tablefansifarvergenericsgetoptggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmeoptparsepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr