Basics | Install TREG | Required knowledge | Asking for help | Citing TREG | Overview | Why are TREGs useful? | What makes a gene a good TREG? | How to find candidate TREGs with TREG | Example TREG Application | Load Packages | Download and Prep Data | Filter and Refine to Cell Types of Interest | Filter Genes | Filter to Top 50% Expression | Calculate Proportion Zero and Pick Cutoff | Filter by the Max Proportion Zero | Run Rank Invariance | Selecting thresholds | Conclusion | Reproducibility | Bibliography
Package: TREG 1.17.0
Louise Huuki-Myers
TREG: Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data
RNA abundance and cell size parameters could improve RNA-seq deconvolution algorithms to more accurately estimate cell type proportions given the different cell type transcription activity levels. A Total RNA Expression Gene (TREG) can facilitate estimating total RNA content using single molecule fluorescent in situ hybridization (smFISH). We developed a data-driven approach using a measure of expression invariance to find candidate TREGs in postmortem human brain single nucleus RNA-seq. This R package implements the method for identifying candidate TREGs from snRNA-seq data.
Authors:
TREG_1.17.0.tar.gz
TREG_1.17.0.zip(r-4.7)TREG_1.17.0.zip(r-4.6)TREG_1.17.0.zip(r-4.5)
TREG_1.17.0.tgz(r-4.6-any)TREG_1.17.0.tgz(r-4.5-any)
TREG_1.17.0.tar.gz(r-4.7-any)TREG_1.17.0.tar.gz(r-4.6-any)
TREG_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TREG/json (API)
| # Install 'TREG' in R: |
| install.packages('TREG', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lieberinstitute/treg/issues
Pkgdown/docs site:https://research.libd.org
Datasets:
- sce_zero_test - Test SummarizedExperiment data
On BioConductor:TREG-1.17.0(bioc 3.24)TREG-1.16.0(bioc 3.23)
softwaresinglecellrnaseqgeneexpressiontranscriptomicstranscriptionsequencingbioconductordeconvolutionrnascopescrna-seqsmfishsnrna-seqtreg
Last updated from:930d109d68. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 197 | ||
| linux-devel-x86_64 | OK | 316 | ||
| source / vignettes | OK | 303 | ||
| linux-release-x86_64 | OK | 237 | ||
| macos-release-arm64 | OK | 237 | ||
| macos-oldrel-arm64 | OK | 156 | ||
| windows-devel | OK | 160 | ||
| windows-release | OK | 197 | ||
| windows-oldrel | OK | 179 | ||
| wasm-release | OK | 133 |
Exports:filter_prop_zeroget_prop_zerorank_cellsrank_grouprank_invariancerank_invariance_express
Dependencies:abindBiobaseBiocGenericsBiocManagercliDelayedArraygenericsGenomicRangesglueIRangeslatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatspurrrrafalibRColorBrewerrlangS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentvctrsXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Filter Genes for by Max Proportion Zero Among Groups | filter_prop_zero |
| Get the Proportion of Zero Counts for Each Gene in Each Group | get_prop_zero |
| Get the Rank of the Expression for each Gene in each Cell | rank_cells |
| Get the Rank of the Mean expression for each Gene in each Group | rank_group |
| Calculate the Rank Invariance of Each Gene from Cell and Group Ranks | rank_invariance |
| Calculate the Rank Invariance of Each Gene from SCE object | rank_invariance_express |
| Test SummarizedExperiment data | sce_zero_test |
