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Xiyu
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^docs$ | ||
^pkgdown$ | ||
^vignettes/articles$ | ||
^\.github$ | ||
^cran-comments\.md$ |
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*.html |
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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | ||
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | ||
on: | ||
push: | ||
branches: [main, master] | ||
pull_request: | ||
branches: [main, master] | ||
|
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name: R-CMD-check | ||
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jobs: | ||
R-CMD-check: | ||
runs-on: ${{ matrix.config.os }} | ||
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name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | ||
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strategy: | ||
fail-fast: false | ||
matrix: | ||
config: | ||
- {os: macos-latest, r: 'release'} | ||
- {os: windows-latest, r: 'release'} | ||
- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} | ||
- {os: ubuntu-latest, r: 'release'} | ||
- {os: ubuntu-latest, r: 'oldrel-1'} | ||
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env: | ||
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
R_KEEP_PKG_SOURCE: yes | ||
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steps: | ||
- uses: actions/checkout@v3 | ||
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- uses: r-lib/actions/setup-pandoc@v2 | ||
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- uses: r-lib/actions/setup-r@v2 | ||
with: | ||
r-version: ${{ matrix.config.r }} | ||
http-user-agent: ${{ matrix.config.http-user-agent }} | ||
use-public-rspm: true | ||
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- uses: r-lib/actions/setup-r-dependencies@v2 | ||
with: | ||
extra-packages: any::rcmdcheck | ||
needs: check | ||
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- uses: r-lib/actions/check-r-package@v2 | ||
with: | ||
upload-snapshots: true |
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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | ||
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | ||
on: | ||
push: | ||
branches: [main, master] | ||
pull_request: | ||
branches: [main, master] | ||
|
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name: test-coverage | ||
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jobs: | ||
test-coverage: | ||
runs-on: ubuntu-latest | ||
env: | ||
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
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steps: | ||
- uses: actions/checkout@v3 | ||
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- uses: r-lib/actions/setup-r@v2 | ||
with: | ||
use-public-rspm: true | ||
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- uses: r-lib/actions/setup-r-dependencies@v2 | ||
with: | ||
extra-packages: any::covr | ||
needs: coverage | ||
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- name: Test coverage | ||
run: | | ||
covr::codecov( | ||
quiet = FALSE, | ||
clean = FALSE, | ||
install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") | ||
) | ||
shell: Rscript {0} | ||
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- name: Show testthat output | ||
if: always() | ||
run: | | ||
## -------------------------------------------------------------------- | ||
find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true | ||
shell: bash | ||
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- name: Upload test results | ||
if: failure() | ||
uses: actions/upload-artifact@v3 | ||
with: | ||
name: coverage-test-failures | ||
path: ${{ runner.temp }}/package |
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Package: SpaTopic | ||
Type: Package | ||
Title: topic inference to identify tissue architecture in multiplexed images | ||
Title: Topic Inference to Identify Tissue Architecture in Multiplexed Images | ||
Version: 0.99 | ||
Date: 2023-12-20 | ||
Author: Xiyu Peng | ||
Maintainer: Xiyu Peng <[email protected]> | ||
Description: Fast topic inference to identify tissue architecture across multiplexed images. | ||
Compared to other KNN-based methods, SpaTopic runs much faster on large-scale image data. | ||
Description: A novel spatial topic model to integrate both cell type and spatial | ||
information to identify the complex spatial tissue architectures on | ||
multiplexed tissue images without human intervention. The Package | ||
implements a Collapsed Gibbs sampling algorithm for inference. | ||
Contrasting to computationally intensive K-nearest-neighbor-based | ||
cell neighborhood analysis approaches, SpaTopic is more scalable | ||
to large-scale image datasets without extracting neighborhood | ||
information for every single cell. | ||
License: GPL (>= 3) | ||
Depends: R (>= 3.5.0), | ||
Rcpp (>= 0.12.0), | ||
RcppArmadillo (>= 0.12.0), | ||
RANN (>= 2.6.0), | ||
Imports: sf (>= 1.0-12), | ||
Imports: RANN (>= 2.6.0), | ||
sf (>= 1.0-12), | ||
methods (>= 3.4), | ||
foreach (>= 1.5.0), | ||
iterators (>= 1.0), | ||
|
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# SpaTopic 0.99 | ||
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||
* Version under development | ||
* The Version under development |
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## R CMD check results | ||
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0 errors | 0 warnings | 1 note | ||
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* This is a new release. |
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