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✨
DESCRIPTION |NEWS
card.svg |card.png
GeoDiff/json (API)

# 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)

geneexpression differentialexpression normalization openblas cpp openmp

6.00 score 9 stars 22 scripts 12 exports 136 dependencies

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

Target	Result	Time
bioc-checks	NOTE	220
linux-devel-arm64	WARNING	360
linux-devel-x86_64	WARNING	452
source / vignettes	OK	497
linux-release-arm64	WARNING	385
linux-release-x86_64	WARNING	441
macos-release-arm64	WARNING	211
macos-release-x86_64	WARNING	595
macos-oldrel-arm64	FAIL	73
macos-oldrel-x86_64	FAIL	284
windows-devel	WARNING	425
windows-release	WARNING	412
windows-oldrel	FAIL	66
wasm-release	OK	220

Exports:aggreprobe BGScoreTest coefNBth contrastNBth DENBth diagPoisBG fitNBth fitNBthDE fitNBthmDE fitPoisBG fitPoisthNorm QuanRange

Dependencies:base64enc beeswarm Biobase BiocGenerics Biostrings boot brio bslib cachem callr cellranger cli codetools cpp11 crayon data.table DEoptimR desc diffobj digest dotCall64 dplyr EnvStats evaluate farver fastmap fit.models fontawesome fontBitstreamVera fontLiberation fontquiver forcats fs future future.apply gdtools generics GeomxTools GGally ggbeeswarm ggiraph ggplot2 ggstats ggthemes globals glue gtable highr hms htmltools htmlwidgets IRanges isoband jquerylib jsonlite knitr labeling lattice lifecycle listenv lme4 lmerTest magrittr MASS Matrix memoise mime minqa mvtnorm NanoStringNCTools nlme nloptr nortest numDeriv otel parallelly patchwork pcaPP pheatmap pillar pkgbuild pkgconfig pkgload plyr praise prettyunits processx progress progressr ps purrr R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack readxl reformulas rematch reshape2 rjson rlang rmarkdown robust robustbase roptim rprojroot rrcov S4Vectors S7 sass scales Seqinfo SeuratObject sp spam stringi stringr systemfonts testthat tibble tidyr tidyselect tinytex utf8 vctrs vipor viridisLite waldo withr xfun XVector yaml

Workflow_WTA

Rendered fromWorkflow_WTA_kidney.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Generate aggregated counts of probes for the same target	aggreprobe aggreprobe,matrix-method aggreprobe,NanoStringGeoMxSet-method
Testing for features above the background	BGScoreTest BGScoreTest,matrix-method BGScoreTest,NanoStringGeoMxSet-method
Testing for features above the background, multiple slides case	BGScoreTest_sp BGScoreTest_sp,matrix-method
Generate list of Wald test inference results on model coefficients	coefNBth coefNBth,list-method
Generate list of Wald test inference results on user specified contrasts	contrastNBth contrastNBth,list-method
A demo dataset for GeoMx Cancer Transcriptome Atlas (CTA) panel	demoData
Generate DE table using the inference list generated by coefNBth or contrastNBth	DENBth DENBth,list-method
Perform diagnosis on Poisson background model	diagPoisBG diagPoisBG,list-method diagPoisBG,NanoStringGeoMxSet-method
Negative Binomial threshold model	fitNBth fitNBth,matrix-method fitNBth,NanoStringGeoMxSet-method
Negative Binomial threshold model for differential expression analysis	fitNBthDE fitNBthDE,matrix-method fitNBthDE,NanoStringGeoMxSet-method
Negative Binomial threshold mixed model for differential expression analysis	fitNBthmDE fitNBthmDE,matrix-method fitNBthmDE,NanoStringGeoMxSet-method
Estimate Poisson background model for either single slide or multiple slides	fitPoisBG fitPoisBG,matrix-method fitPoisBG,NanoStringGeoMxSet-method
Estimate Poisson background model for multiple slides	fitPoisBG_sp fitPoisBG_sp,matrix-method
Poisson threshold model based normalization-log2 transformation for single slide or for multiple slides	fitPoisthNorm fitPoisthNorm,matrix-method fitPoisthNorm,NanoStringGeoMxSet-method
Poisson threshold model based normalization-log2 transformation for multiple slides	fitPoisthNorm_sp fitPoisthNorm_sp,matrix-method
A demo dataset for GeoMx Human Whole Transcriptome Atlas (WTA) panel	kidney
A demo example output list returned by function fitNBthDE	NBthDEmod2
A demo example output list returned by function fitNBthmDE	NBthmDEmod2
A demo example output list returned by function fitNBthmDE	NBthmDEmod2slope
Compute Quantile Range	QuanRange QuanRange,matrix-method QuanRange,NanoStringGeoMxSet-method