Package: STREAK 1.0.0
Azka Javaid
STREAK: Receptor Abundance Estimation using Feature Selection and Gene Set Scoring
Performs receptor abundance estimation for single cell RNA-sequencing data using a supervised feature selection mechanism and a thresholded gene set scoring procedure. Seurat's normalization method is described in: Hao et al., (2021) <doi:10.1016/j.cell.2021.04.048>, Stuart et al., (2019) <doi:10.1016/j.cell.2019.05.031>, Butler et al., (2018) <doi:10.1038/nbt.4096> and Satija et al., (2015) <doi:10.1038/nbt.3192>. Method for reduced rank reconstruction and rank-k selection is detailed in: Javaid et al., (2022) <doi:10.1101/2022.10.08.511197>. Gene set scoring procedure is described in: Frost et al., (2020) <doi:10.1093/nar/gkaa582>. Clustering method is outlined in: Song et al., (2020) <doi:10.1093/bioinformatics/btaa613> and Wang et al., (2011) <doi:10.32614/RJ-2011-015>.
Authors:
STREAK_1.0.0.tar.gz
STREAK_1.0.0.tar.gz(r-4.5-noble)STREAK_1.0.0.tar.gz(r-4.4-noble)
STREAK_1.0.0.tgz(r-4.4-emscripten)
STREAK.pdf |STREAK.html✨
STREAK/json (API)
| # Install 'STREAK' in R: |
| install.packages('STREAK', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- target.malt.rna.mat - Single cell RNA-sequencing (scRNA-seq) target subset of the 10X Genomics MALT counts.
- train.malt.adt.mat - Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) training subset of the 10X Genomics MALT counts.
- train.malt.rna.mat - Single cell RNA-sequencing (scRNA-seq) training subset of the 10X Genomics MALT counts.
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 10 months agofrom:c8976a53da. Checks:OK: 1 WARNING: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 13 2024 |
| R-4.5-linux | WARNING | Sep 13 2024 |
Exports:receptorAbundanceEstimationreceptorGeneSetConstruction
Dependencies:abindaskpassbase64encBHbitopsbslibcachemcaToolsCkmeans.1d.dpcliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsrbibutilsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLRdpackreshape2reticulaterlangrmarkdownROCRrprojrootRSpectrarsvdRtsnesassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsSPECKstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotVAMvctrsviridisLitewithrxfunxtableyamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Receptor abundance estimation for single cell RNA-sequencing (scRNA-seq) data using gene set scoring and thresholding. | receptorAbundanceEstimation |
| Gene sets weights membership matrix construction for receptor abundance estimation. | receptorGeneSetConstruction |
| Single cell RNA-sequencing (scRNA-seq) target subset of the 10X Genomics MALT counts. | target.malt.rna.mat |
| Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) training subset of the 10X Genomics MALT counts. | train.malt.adt.mat |
| Single cell RNA-sequencing (scRNA-seq) training subset of the 10X Genomics MALT counts. | train.malt.rna.mat |