Package: HDStIM 1.0.0

Rohit Farmer

HDStIM: High Dimensional Stimulation Immune Mapping ('HDStIM')

A method for identifying responses to experimental stimulation in mass or flow cytometry that uses high dimensional analysis of measured parameters and can be performed with an end-to-end unsupervised approach. In the context of in vitro stimulation assays where high-parameter cytometry was used to monitor intracellular response markers, using cell populations annotated either through automated clustering or manual gating for a combined set of stimulated and unstimulated samples, 'HDStIM' labels cells as responding or non-responding. The package also provides auxiliary functions to rank intracellular markers based on their contribution to identifying responses and generating diagnostic plots.

Authors:Rohit Farmer [aut, cre], Richard Apps [aut], John Tsang [aut, pdr]

HDStIM_1.0.0.tar.gz
HDStIM_1.0.0.zip(r-4.7)HDStIM_1.0.0.zip(r-4.6)HDStIM_1.0.0.zip(r-4.5)
HDStIM_1.0.0.tgz(r-4.6-any)HDStIM_1.0.0.tgz(r-4.5-any)
HDStIM_1.0.0.tar.gz(r-4.7-any)HDStIM_1.0.0.tar.gz(r-4.6-any)
HDStIM_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
HDStIM/json (API)

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

Bug tracker:https://github.com/niaid/hdstim/issues

Pkgdown/docs site:https://niaid.github.io

Datasets:
  • chi11 - Sample data set for CyTOF Stimulation Assay

On CRAN:

Conda:

complexheatmapassaycytofcytometrycytometry-analysis-pipelineflowcytometrystimulation

4.71 score 3 stars 17 scripts 186 downloads 6 exports 67 dependencies

Last updated from:b42e3d8387. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK264
source / vignettesOK306
linux-release-x86_64OK274
macos-release-arm64OK205
macos-oldrel-arm64OK197
windows-develOK223
windows-releaseOK209
windows-oldrelOK195
wasm-releaseOK165

Exports:HDStIMmarker_ranking_borutaplot_exprsplot_K_Fisherplot_marker_ranking_heatmapplot_umap

Dependencies:backportsBHBiocGenericsBorutabroomcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayondigestdoParalleldplyrdqrngfarverFNNforeachfrugenericsGetoptLongggplot2ggridgesGlobalOptionsgluegtableIRangesirlbaisobanditeratorslabelinglatticelifecyclemagrittrMatrixmatrixStatspillarpkgconfigpngpurrrR6RColorBrewerRcppRcppAnnoyRcppEigenRcppProgressrjsonrlangRSpectraS4VectorsS7scalesshapesitmostringistringrtibbletidyrtidyselectutf8uwotvctrsviridisLitewithr

HDStIM

Rohit Farmer

Rendered fromHDStIM.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2022-05-13
Started: 2022-04-14