https://github.com/bioconductor-source/retrofit
Science Score: 13.0%
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○Scientific vocabulary similarity
Low similarity (5.7%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- Language: R
- Default Branch: devel
- Size: 2.99 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
RETROFIT enables reference-free cell-type deconvolution of spatial transcriptomics data.
Installation
Install retrofit from github:
r
install.packages("devtools")
devtools::install_github("qunhualilab/retrofit")
Install retrofit from Bioconductor.
```{r} if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install(version='devel') BiocManager::install("retrofit") ```
Example
``` r library(retrofit)
load built in data
data(testSimulationData) x = testSimulationData$extra5x scref = testSimulationData$scref markerref = testSimulationData$marker_ref
decompose
res = retrofit::decompose(x, L=16, iterations=100, verbose=TRUE) W = res$w H = res$h TH = res$th
annotate with correlations
res = retrofit::annotateWithCorrelations(scref, K=8, decompw=W, decomph=H) Wannotated = res$w Hannotated = res$h cells = res$rankedcells
annotate with markers
res = retrofit::annotateWithMarkers(markerref, K=8, decompw=W, decomph=H)
Wannotated = res$w
Hannotated = res$h
cells = res$rankedcells
```
More details can be found in the vignettes. - Simulation Vignette - Colon Vignette
Owner
- Name: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
Source code for packages accepted into Bioconductor
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Dependencies
- R >= 4.2 depends
- Rcpp * depends
- BiocStyle * suggests
- DescTools * suggests
- RCurl * suggests
- colorspace * suggests
- corrplot * suggests
- cowplot * suggests
- ggplot2 * suggests
- grid * suggests
- knitr * suggests
- pals * suggests
- png * suggests
- reshape2 * suggests
- rmarkdown * suggests
- testthat * suggests