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-4.5)HDStIM_1.0.0.zip(r-4.4)HDStIM_1.0.0.zip(r-4.3)
HDStIM_1.0.0.tgz(r-4.4-any)HDStIM_1.0.0.tgz(r-4.3-any)
HDStIM_1.0.0.tar.gz(r-4.5-noble)HDStIM_1.0.0.tar.gz(r-4.4-noble)
HDStIM_1.0.0.tgz(r-4.4-emscripten)HDStIM_1.0.0.tgz(r-4.3-emscripten)
HDStIM.pdf |HDStIM.html✨
HDStIM/json (API)

Peer review:

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

On CRAN:

complexheatmapassaycytofcytometrycytometry-analysis-pipelineflowcytometrystimulation

6 exports 3 stars 1.10 score 71 dependencies 17 scripts 218 downloads

Last updated 12 months agofrom:b42e3d8387. Checks:OK: 6 ERROR: 1. Indexed: yes.

Exports:HDStIMmarker_ranking_borutaplot_exprsplot_K_Fisherplot_marker_ranking_heatmapplot_umap

Dependencies:backportsBHBiocGenericsBorutabroomcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayondigestdoParalleldplyrdqrngfansifarverFNNforeachgenericsGetoptLongggplot2ggridgesGlobalOptionsgluegtableIRangesirlbaisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmgcvmunsellnlmepillarpkgconfigpngpurrrR6rangerRColorBrewerRcppRcppAnnoyRcppEigenRcppProgressrjsonrlangRSpectraS4Vectorsscalesshapesitmostringistringrtibbletidyrtidyselectutf8uwotvctrsviridisLitewithr