Package: mineCitrus 1.0.0

Allison Throm

mineCitrus: Extract and Analyze Median Molecule Intensity from 'citrus' Output

Citrus is a computational technique developed for the analysis of high dimensional cytometry data sets. This package extracts, statistically analyzes, and visualizes marker expression from 'citrus' data. This code was used to generate data for Figures 3 and 4 in the forthcoming manuscript: Throm et al. “Identification of Enhanced Interferon-Gamma Signaling in Polyarticular Juvenile Idiopathic Arthritis with Mass Cytometry”, JCI-Insight. For more information on Citrus, please see: Bruggner et al. (2014) <doi:10.1073/pnas.1408792111>. To download the 'citrus' package, please see <https://github.com/nolanlab/citrus>.

Authors:Allison Throm

mineCitrus_1.0.0.tar.gz
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mineCitrus.pdf |mineCitrus.html✨
mineCitrus/json (API)

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

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

1.00 score 40 scripts 97 downloads 13 exports 28 dependencies

Last updated 6 years agofrom:e1dfedf4ab. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 15 2024
R-4.5-linuxOKDec 15 2024

Exports:allmedsclassclustermedsclustermedsdifMarkerPlotsdifMarkerPlots2filterMarkerfindclustfindSigplotdifplotdif2posthocprocessforanovasortmat

Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Gets matrices of medians for each individual sample for all measured parameters for all clustersallmeds
Cytometry data set for example of Citrus data set from nolanlab/citruscitrus.combinedFCSSet
Clustering data for example of Citrus data set from nolanlab/citruscitrus.foldClustering
Correlation data for example of Citrus data set from nolanlab/citruscitrus.foldFeatureSet
Gets matrices of medians for each individual sample for all measured parameters for all clustersclassclustermeds
Gets matrix of medians for desired measured features for all clusters meeting threshold requirements specified in Citrusclustermeds
Plot dot plots of features where both clusters are significantly different from the reference cluster without processing data before handdifMarkerPlots
Plot dot plots of features where one cluster is significantly different from the reference cluster without processing data before handdifMarkerPlots2
Filters list of data matrices with columns corresponding to the measured parameters of interestfilterMarker
Filters list to contain only desired clustersfindclust
Assesses significance of ANOVA and t-test resultsfindSig
Plot dot plots of features where both clusters are significantly different from the reference clusterplotdif
Plot dot plots of features where one cluster is significantly different from the reference clusterplotdif2
Runs ANOVA and t-tests comparing clusters and markers in clustersposthoc
Processes cluster signaling data in form for statistical analysisprocessforanova
Reorders to rows (corresponding to different clusters) of a matrix of medians to a desired ordersortmat