Package: GeoDiff 1.19.0

Maddy Griswold

GeoDiff: Count model based differential expression and normalization on GeoMx RNA data

A series of statistical models using count generating distributions for background modelling, feature and sample QC, normalization and differential expression analysis on GeoMx RNA data. The application of these methods are demonstrated by example data analysis vignette.

Authors:Maddy Griswold [cre], Lei Yang [aut], Zhi Yang [aut]

GeoDiff_1.19.0.tar.gz
GeoDiff_1.19.0.zip(r-4.7)GeoDiff_1.19.0.zip(r-4.6)GeoDiff_1.17.0.zip(r-4.5)
GeoDiff_1.19.0.tgz(r-4.6-x86_64)GeoDiff_1.19.0.tgz(r-4.6-arm64)GeoDiff_1.17.0.tgz(r-4.5-x86_64)GeoDiff_1.17.0.tgz(r-4.5-arm64)
GeoDiff_1.19.0.tar.gz(r-4.7-arm64)GeoDiff_1.19.0.tar.gz(r-4.7-x86_64)GeoDiff_1.19.0.tar.gz(r-4.6-arm64)GeoDiff_1.19.0.tar.gz(r-4.6-x86_64)
GeoDiff_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
GeoDiff/json (API)
NEWS

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

Bug tracker:https://github.com/nanostring-biostats/geodiff/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • demoData - A demo dataset for GeoMx Cancer Transcriptome Atlas (CTA) panel
  • kidney - A demo dataset for GeoMx Human Whole Transcriptome Atlas (WTA) panel
  • NBthDEmod2 - A demo example output list returned by function fitNBthDE
  • NBthmDEmod2 - A demo example output list returned by function fitNBthmDE
  • NBthmDEmod2slope - A demo example output list returned by function fitNBthmDE

On BioConductor:GeoDiff-1.19.0(bioc 3.24)GeoDiff-1.18.0(bioc 3.23)

geneexpressiondifferentialexpressionnormalizationopenblascppopenmp

5.93 score 9 stars 19 scripts 306 downloads 12 exports 135 dependencies

Last updated from:ea81008f7d. Checks:1 NOTE, 8 WARNING, 2 OK, 3 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE296
linux-devel-arm64WARNING393
linux-devel-x86_64WARNING525
source / vignettesOK446
linux-release-arm64WARNING368
linux-release-x86_64WARNING356
macos-release-arm64WARNING251
macos-release-x86_64WARNING688
macos-oldrel-arm64FAIL72
macos-oldrel-x86_64FAIL296
windows-develWARNING434
windows-releaseWARNING436
windows-oldrelFAIL77
wasm-releaseOK185

Exports:aggreprobeBGScoreTestcoefNBthcontrastNBthDENBthdiagPoisBGfitNBthfitNBthDEfitNBthmDEfitPoisBGfitPoisthNormQuanRange

Dependencies:base64encbeeswarmBiobaseBiocGenericsBiostringsbootbriobslibcachemcallrcellrangerclicodetoolscpp11crayondata.tableDEoptimRdescdiffobjdigestdotCall64dplyrEnvStatsevaluatefarverfastmapfit.modelsfontawesomefontBitstreamVerafontLiberationfontquiverforcatsfsfuturefuture.applygdtoolsgenericsGeomxToolsGGallyggbeeswarmggiraphggplot2ggstatsggthemesglobalsgluegtablehighrhmshtmltoolshtmlwidgetsIRangesisobandjquerylibjsonliteknitrlabelinglatticelifecyclelistenvlme4lmerTestmagrittrMASSMatrixmemoisemimeminqamvtnormNanoStringNCToolsnlmenloptrnortestnumDerivparallellypatchworkpcaPPpheatmappillarpkgbuildpkgconfigpkgloadplyrpraiseprettyunitsprocessxprogressprogressrpspurrrR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadxlreformulasrematchreshape2rjsonrlangrmarkdownrobustrobustbaseroptimrprojrootrrcovS4VectorsS7sassscalesSeqinfoSeuratObjectspspamstringistringrsystemfontstestthattibbletidyrtidyselecttinytexutf8vctrsviporviridisLitewaldowithrxfunXVectoryaml

Workflow_WTA

Rendered fromWorkflow_WTA_kidney.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2022-04-18
Started: 2021-10-01

Readme and manuals

Help Manual

Help pageTopics
Generate aggregated counts of probes for the same targetaggreprobe aggreprobe,matrix-method aggreprobe,NanoStringGeoMxSet-method
Testing for features above the backgroundBGScoreTest BGScoreTest,matrix-method BGScoreTest,NanoStringGeoMxSet-method
Testing for features above the background, multiple slides caseBGScoreTest_sp BGScoreTest_sp,matrix-method
Generate list of Wald test inference results on model coefficientscoefNBth coefNBth,list-method
Generate list of Wald test inference results on user specified contrastscontrastNBth contrastNBth,list-method
A demo dataset for GeoMx Cancer Transcriptome Atlas (CTA) paneldemoData
Generate DE table using the inference list generated by coefNBth or contrastNBthDENBth DENBth,list-method
Perform diagnosis on Poisson background modeldiagPoisBG diagPoisBG,list-method diagPoisBG,NanoStringGeoMxSet-method
Negative Binomial threshold modelfitNBth fitNBth,matrix-method fitNBth,NanoStringGeoMxSet-method
Negative Binomial threshold model for differential expression analysisfitNBthDE fitNBthDE,matrix-method fitNBthDE,NanoStringGeoMxSet-method
Negative Binomial threshold mixed model for differential expression analysisfitNBthmDE fitNBthmDE,matrix-method fitNBthmDE,NanoStringGeoMxSet-method
Estimate Poisson background model for either single slide or multiple slidesfitPoisBG fitPoisBG,matrix-method fitPoisBG,NanoStringGeoMxSet-method
Estimate Poisson background model for multiple slidesfitPoisBG_sp fitPoisBG_sp,matrix-method
Poisson threshold model based normalization-log2 transformation for single slide or for multiple slidesfitPoisthNorm fitPoisthNorm,matrix-method fitPoisthNorm,NanoStringGeoMxSet-method
Poisson threshold model based normalization-log2 transformation for multiple slidesfitPoisthNorm_sp fitPoisthNorm_sp,matrix-method
A demo dataset for GeoMx Human Whole Transcriptome Atlas (WTA) panelkidney
A demo example output list returned by function fitNBthDENBthDEmod2
A demo example output list returned by function fitNBthmDENBthmDEmod2
A demo example output list returned by function fitNBthmDENBthmDEmod2slope
Compute Quantile RangeQuanRange QuanRange,matrix-method QuanRange,NanoStringGeoMxSet-method