From 68e365ad9718d35c6d612e97448f0f2c8eef4784 Mon Sep 17 00:00:00 2001 From: Xiyu Date: Fri, 19 Jan 2024 16:34:43 -0500 Subject: [PATCH] Update info for installation --- DESCRIPTION | 2 +- README.md | 8 +++++++- docs/404.html | 2 +- docs/LICENSE.html | 2 +- docs/articles/Intro_SpaTopic.html | 2 +- docs/articles/Model_Selection.html | 2 +- docs/articles/SpaTopic.html | 4 ++-- docs/articles/index.html | 2 +- docs/authors.html | 6 +++--- docs/index.html | 15 +++++++++------ docs/news/index.html | 3 ++- docs/pkgdown.yml | 2 +- docs/reference/Seurat5obj_to_SpaTopic.html | 2 +- docs/reference/SpaTopic-Package.html | 2 +- docs/reference/SpaTopic_inference.html | 2 +- docs/reference/gibbs.res-class.html | 2 +- docs/reference/index.html | 2 +- docs/reference/lung5.html | 2 +- docs/reference/stratified_sampling_sf.html | 2 +- docs/search.json | 2 +- 20 files changed, 38 insertions(+), 28 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 1e412df..b9b0abd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -5,7 +5,7 @@ Version: 1.0.1.9000 Date: 2023-12-20 Authors@R: person("Xiyu", "Peng", email = "pansypeng124@gmail.com", role = c("aut", "cre"),comment = c(ORCID = "0000-0003-4232-0910")) -Description: A novel spatial topic model to integrate both cell type and spatial information to identify the complex spatial tissue architecture on multiplexed tissue images without human intervention. The Package implements a Collapsed Gibbs sampling algorithm for inference. 'SpaTopic' is scalable to large-scale image datasets without extracting neighborhood information for every single cell. For more details on the methodology, see . +Description: A novel spatial topic model to integrate both cell type and spatial information to identify the complex spatial tissue architecture on multiplexed tissue images without human intervention. The Package implements a collapsed Gibbs sampling algorithm for inference. 'SpaTopic' is scalable to large-scale image datasets without extracting neighborhood information for every single cell. For more details on the methodology, see . License: GPL (>= 3) Depends: R (>= 3.5.0), Imports: Rcpp (>= 0.12.0), diff --git a/README.md b/README.md index a453039..2e314fb 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,13 @@ Compared to other KNN-based methods (such as KNN-kmeans, the default in Seurat v ## Installation -`SpaTopic` can be installed from the [GitHub repository](https://github.com/xiyupeng/SpaTopic) using the devtools package. +The R package `SpaTopic` now is available in CRAN and can be installed with the following code. + +``` r +install.packages("SpaTopic") +``` + +The development version of `SpaTopic` can be installed from the [GitHub repository](https://github.com/xiyupeng/SpaTopic). ``` r # install.packages("devtools") diff --git a/docs/404.html b/docs/404.html index 4017427..6d9a040 100644 --- a/docs/404.html +++ b/docs/404.html @@ -24,7 +24,7 @@ SpaTopic - 1.0.1 + 1.0.1.9000