Package: GeoDiff 1.11.0

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_1.11.0.tar.gz
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GeoDiff_1.11.0.tgz(r-4.4-emscripten)
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'))

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-1.11.0(bioc 3.20)GeoDiff-1.10.0(bioc 3.19)

bioconductor-package

12 exports 0.82 score 152 dependencies

Last updated 2 months agofrom:c1d6199697

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

Dependencies:askpass backports base64enc beeswarm Biobase BiocGenerics Biostrings bit bit64 boot brio broom broom.helpers bslib cachem callr cellranger cli clipr codetools colorspace cpp11 crayon curl data.table DEoptimR desc diffobj digest dotCall64 dplyr EnvStats evaluate fansi farver fastmap fit.models fontawesome forcats fs future future.apply generics GenomeInfoDb GenomeInfoDbData GeomxTools GGally ggbeeswarm ggiraph ggplot2 ggstats ggthemes globals glue gtable haven highr hms htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite knitr labeling labelled lattice lifecycle listenv lme4 lmerTest magrittr MASS Matrix memoise mgcv mime minqa munsell mvtnorm NanoStringNCTools nlme nloptr nortest numDeriv openssl parallelly patchwork pcaPP pheatmap pillar pkgbuild pkgconfig pkgload plyr praise prettyunits processx progress progressr ps purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen readr readxl rematch rematch2 reshape2 rjson rlang rmarkdown robust robustbase roptim rprojroot rrcov S4Vectors sass scales SeuratObject sp spam stringi stringr sys systemfonts testthat tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 uuid vctrs vipor viridisLite vroom waldo withr xfun XVector yaml zlibbioc

Workflow_WTA

Rendered fromWorkflow_WTA_kidney.Rmdusingknitr::rmarkdownon Jun 12 2024.

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