Simulate a small dataset with known answers | 1. Build the reference | 2. Deconvolve | 3. Check against the truth | Larger data | Reference
Package: spatialDWLS 0.1.1
Ruben Dries
spatialDWLS: Cell Type Deconvolution of Spatial Transcriptomics with Dampened Weighted Least Squares
Estimates the cell type composition of each spot of a spatial transcriptomics experiment from a single-cell reference, following spatialDWLS (Dong and Yuan 2021, <doi:10.1186/s13059-021-02362-7>), which builds on dampened weighted least squares (DWLS; Tsoucas et al. 2019, <doi:10.1038/s41467-019-10802-z>). Spots are solved in two rounds: candidate cell types are chosen per cluster by enrichment, then each spot is re-solved against the types present in it. Works on dense or sparse matrices, in parallel through 'BiocParallel', and over windows of spots for expression stores that do not fit in memory.
Authors:
spatialDWLS_0.1.1.tar.gz
spatialDWLS_0.1.1.zip(r-4.7-any)spatialDWLS_0.1.1.zip(r-4.6-any)spatialDWLS_0.1.1.zip(r-4.5-any)
spatialDWLS_0.1.1.tgz(r-4.6-any)spatialDWLS_0.1.1.tgz(r-4.5-any)
spatialDWLS_0.1.1.tar.gz(r-4.7-any)spatialDWLS_0.1.1.tar.gz(r-4.6-any)
spatialDWLS_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
spatialDWLS/json (API)
| # Install 'spatialDWLS' in R: |
| install.packages('spatialDWLS', repos = c('https://drieslab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/drieslab/spatialdwls/issues
Pkgdown/docs site:https://drieslab.github.io
Last updated from:45d201da6a. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 126 | ||
| source / vignettes | OK | 175 | ||
| linux-release | OK | 125 | ||
| macos-release | OK | 129 | ||
| macos-oldrel | OK | 90 | ||
| windows-devel | OK | 91 | ||
| windows-release | OK | 94 | ||
| windows-oldrel | OK | 90 | ||
| wasm-release | OK | 99 |
Exports:dwlsdwls_signaturedwls_stream
Dependencies:latticeMatrixMatrixGenericsmatrixStatsquadprog
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Deconvolve spots into cell type proportions | dwls |
| Build a DWLS signature matrix | dwls_signature |
| Deconvolve spots read in windows | dwls_stream |