Package: glmGamPoi 1.24.0
Constantin Ahlmann-Eltze
glmGamPoi: Fit a Gamma-Poisson Generalized Linear Model
Fit linear models to overdispersed count data. The package can estimate the overdispersion and fit repeated models for matrix input. It is designed to handle large input datasets as they typically occur in single cell RNA-seq experiments.
Authors:
glmGamPoi_1.24.0.tar.gz
glmGamPoi_1.24.0.zip(r-4.7)glmGamPoi_1.24.0.zip(r-4.6)glmGamPoi_1.24.0.zip(r-4.5)
glmGamPoi_1.24.0.tgz(r-4.6-x86_64)glmGamPoi_1.24.0.tgz(r-4.6-arm64)glmGamPoi_1.24.0.tgz(r-4.5-x86_64)glmGamPoi_1.24.0.tgz(r-4.5-arm64)
glmGamPoi_1.24.0.tar.gz(r-4.7-arm64)glmGamPoi_1.24.0.tar.gz(r-4.7-x86_64)glmGamPoi_1.24.0.tar.gz(r-4.6-arm64)glmGamPoi_1.24.0.tar.gz(r-4.6-x86_64)
glmGamPoi_1.24.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
glmGamPoi/json (API)
NEWS
| # Install 'glmGamPoi' in R: |
| install.packages('glmGamPoi', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/const-ae/glmgampoi/issues
On BioConductor:glmGamPoi-1.25.1(bioc 3.24)glmGamPoi-1.24.0(bioc 3.23)
regressionrnaseqsoftwaresinglecellgamma-poissonglmnegative-binomial-regressionon-diskopenblascpp
Last updated from:ce78f68693 (on RELEASE_3_23). Checks:9 WARNING, 3 ERROR, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 267 | ||
| linux-devel-arm64 | ERROR | 347 | ||
| linux-devel-x86_64 | ERROR | 437 | ||
| source / vignettes | OK | 671 | ||
| linux-release-arm64 | WARNING | 350 | ||
| linux-release-x86_64 | WARNING | 377 | ||
| macos-release-arm64 | WARNING | 206 | ||
| macos-release-x86_64 | WARNING | 359 | ||
| macos-oldrel-arm64 | WARNING | 237 | ||
| macos-oldrel-x86_64 | WARNING | 358 | ||
| windows-devel | ERROR | 1113 | ||
| windows-release | WARNING | 1026 | ||
| windows-oldrel | WARNING | 965 | ||
| wasm-release | OK | 217 |
Exports:glm_gploc_median_fitoverdispersion_mleoverdispersion_shrinkagepseudobulktest_devars
Dependencies:abindassortheadbeachmatBiobaseBiocGenericsbiocmakecliDelayedArrayDelayedMatrixStatsdir.expiryfilelockgenericsGenomicRangesglueh5mreadHDF5ArrayIRangeslatticelifecycleMatrixMatrixGenericsmatrixStatsRcppRcppArmadillorhdf5rhdf5filtersRhdf5librlangS4ArraysS4VectorsSeqinfoSingleCellExperimentSparseArraysparseMatrixStatsSummarizedExperimentvctrsXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert glmGamPoi object to a list | as.list.glmGamPoi |
| Fit a Gamma-Poisson Generalized Linear Model | glm_gp |
| Estimate local median fit | loc_median_fit |
| Estimate the Overdispersion for a Vector of Counts | overdispersion_mle |
| Shrink the overdispersion estimates | overdispersion_shrinkage |
| Predict 'link' or 'response' values for Gamma-Poisson GLMs | predict.glmGamPoi |
| Pretty print the result from glm_gp() | format.glmGamPoi format.summary.glmGamPoi print.glmGamPoi print.summary.glmGamPoi summary.glmGamPoi |
| Create a 'SingleCellExperiment' containing pseudo-bulk samples | pseudobulk |
| Extract Residuals of Gamma Poisson Model | residuals.glmGamPoi |
| Solve the equation Y = A B for A or B | solve_lm_for_A solve_lm_for_B |
| Test for Differential Expression | test_de |
| Quote grouping variables | vars |
