Package: TREG 1.11.0
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_1.11.0.tar.gz
TREG_1.11.0.zip(r-4.5)TREG_1.11.0.zip(r-4.4)TREG_1.11.0.zip(r-4.3)
TREG_1.11.0.tgz(r-4.4-any)TREG_1.11.0.tgz(r-4.3-any)
TREG_1.11.0.tar.gz(r-4.5-noble)TREG_1.11.0.tar.gz(r-4.4-noble)
TREG_1.11.0.tgz(r-4.4-emscripten)TREG_1.11.0.tgz(r-4.3-emscripten)
TREG.pdf |TREG.html✨
TREG/json (API)
NEWS
| # 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
- sce_zero_test - Test SummarizedExperiment data
On BioConductor:TREG-1.11.0(bioc 3.21)TREG-1.10.0(bioc 3.20)
softwaresinglecellrnaseqgeneexpressiontranscriptomicstranscriptionsequencingbioconductordeconvolutionrnascopescrna-seqsmfishsnrna-seqtreg
Last updated 22 days agofrom:2c1d897619. Checks:OK: 4 WARNING: 3. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | WARNING | Oct 31 2024 |
| R-4.5-linux | OK | Oct 31 2024 |
| R-4.4-win | WARNING | Oct 31 2024 |
| R-4.4-mac | OK | Oct 31 2024 |
| R-4.3-win | WARNING | Oct 31 2024 |
| R-4.3-mac | OK | Oct 31 2024 |
Exports:filter_prop_zeroget_prop_zerorank_cellsrank_grouprank_invariancerank_invariance_express
Dependencies:abindaskpassBiobaseBiocGenericsclicrayoncurlDelayedArraygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpurrrR6rafalibRColorBrewerrlangS4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsvctrsXVectorzlibbioc
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 |
