Package: GeoDiff 1.13.0

Nicole Ortogero

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:Nicole Ortogero [cre], Lei Yang [aut], Zhi Yang [aut]

GeoDiff_1.13.0.tar.gz
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GeoDiff.pdf |GeoDiff.html✨
GeoDiff/json (API)
NEWS

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

Peer review:

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:
  • 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
  • demoData - A demo dataset for GeoMx Cancer Transcriptome Atlas (CTA) panel
  • kidney - A demo dataset for GeoMx Human Whole Transcriptome Atlas (WTA) panel

On BioConductor:GeoDiff-1.13.0(bioc 3.21)GeoDiff-1.12.0(bioc 3.20)

geneexpressiondifferentialexpressionnormalizationopenblascppopenmp

5.51 score 8 stars 9 scripts 184 downloads 12 exports 140 dependencies

Last updated 2 months agofrom:e81e283553. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-win-x86_64NOTENov 29 2024
R-4.5-linux-x86_64NOTENov 29 2024
R-4.4-win-x86_64NOTENov 29 2024
R-4.4-mac-x86_64NOTENov 29 2024
R-4.4-mac-aarch64NOTENov 29 2024
R-4.3-win-x86_64NOTENov 29 2024
R-4.3-mac-x86_64NOTENov 29 2024
R-4.3-mac-aarch64NOTENov 29 2024

Exports:aggreprobeBGScoreTestcoefNBthcontrastNBthDENBthdiagPoisBGfitNBthfitNBthDEfitNBthmDEfitPoisBGfitPoisthNormQuanRange

Dependencies:askpassbase64encbeeswarmBiobaseBiocGenericsBiostringsbootbriobslibcachemcallrcellrangerclicodetoolscolorspacecpp11crayoncurldata.tableDEoptimRdescdiffobjdigestdotCall64dplyrEnvStatsevaluatefansifarverfastmapfit.modelsfontawesomeforcatsfsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGeomxToolsGGallyggbeeswarmggiraphggplot2ggstatsggthemesglobalsgluegtablehighrhmshtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteknitrlabelinglatticelifecyclelistenvlme4lmerTestmagrittrMASSMatrixmemoisemgcvmimeminqamunsellmvtnormNanoStringNCToolsnlmenloptrnortestnumDerivopensslparallellypatchworkpcaPPpheatmappillarpkgbuildpkgconfigpkgloadplyrpraiseprettyunitsprocessxprogressprogressrpspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenreadxlrematchreshape2rjsonrlangrmarkdownrobustrobustbaseroptimrprojrootrrcovS4VectorssassscalesSeuratObjectspspamstringistringrsyssystemfontstestthattibbletidyrtidyselecttinytexUCSC.utilsutf8uuidvctrsviporviridisLitewaldowithrxfunXVectoryamlzlibbioc

Workflow_WTA

Rendered fromWorkflow_WTA_kidney.Rmdusingknitr::rmarkdownon Nov 29 2024.

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