Deconvolution of spatial transcriptomics at single-cell resolution.
- This package is still under development. Now the basic functions are complete and we will include more functions and refinement in the future.
- To see codes analyzing the paper, please refer to https://codeocean.com/capsule/1351962/tree/v1.
08/21/2023: The first official version (v1.1.0) of Redeconve is released on Github.
12/01/2023: The article was published in the journal nature communications (https://www.nature.com/articles/s41467-023-43600-9).
04/01/2024: Version v1.1.1 is released with minor bugfixes and new functions about co-localization.
06/07/2024: Version v1.1.2 is released. In this version, all non-R codes are deleted, making this package no longer needs compilation.
Please use the following codes to install Redeconve:
# install.packages("devtools")
devtools::install_github("ZxZhou4150/Redeconve", build_vignettes = F)
You may also set build_vignettes as T, but it may take some time to build the vignette (tens of minutes).
browseVignettes("Redeconve")
!Note on 06/07/2024!
Setting build_vignettes as T may encounter this error:
Error in graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted, :
At vendor/cigraph/src/constructors/adjacency.c:535 : Adjacency matrix should be symmetric to produce an undirected graph. Invalid value
This is not solved yet (actually the passed adjacency matrix IS symmetric). So please don't build the vignette at this time. See the next section for a rendered manual.
If you didn't build the vignette, you can refer [here](Redeconve manual.ipynb) for jupyter notebook and here for the rendered html page.