diff --git a/.DS_Store b/.DS_Store deleted file mode 100644 index eef3e8f..0000000 Binary files a/.DS_Store and /dev/null differ diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml index 0c17b8d..6355403 100644 --- a/.github/workflows/rworkflows.yml +++ b/.github/workflows/rworkflows.yml @@ -12,6 +12,8 @@ name: rworkflows - RELEASE_** jobs: rworkflows: + permissions: + contents: write runs-on: ${{ matrix.config.os }} name: ${{ matrix.config.os }} (${{ matrix.config.r }}) container: ${{ matrix.config.cont }} @@ -31,12 +33,6 @@ jobs: r: latest bioc: release steps: - - if: ${{ env.ACT }} - name: Hack container for local development - run: | - curl -fsSL https://deb.nodesource.com/setup_18.x | sudo -E bash - - sudo apt-get install -y nodejs - shell: bash {0} - uses: neurogenomics/rworkflows@master with: run_bioccheck: ${{ false }} @@ -47,7 +43,7 @@ jobs: run_covr: ${{ true }} run_pkgdown: ${{ true }} has_runit: ${{ false }} - GITHUB_TOKEN: ${{ secrets.PAT_GITHUB }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} run_docker: ${{ true }} docker_user: fulongyu docker_org: fulongyu diff --git a/.gitignore b/.gitignore index 26c90b9..79d5f3f 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,12 @@ .Ruserdata Meta vignettes/*_cache$ + +# find . -name .DS_Store -print0 | xargs -0 git rm -f --ignore-unmatch +./.DS_Store +./**/.DS_Store +./**/**/.DS_Store +./**/**/**/.DS_Store +./**/**/**/**/.DS_Store +./**/**/**/**/**/.DS_Store +./**/**/**/**/**/**/.DS_Store diff --git a/DESCRIPTION b/DESCRIPTION index cd90a14..469a0b2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -4,18 +4,24 @@ Version: 1.0.2 Date: 2020-01-01 URL: https://github.com/sankaranlab/SCAVENGE Authors@R: - person(given = "Fulong", + c(person(given = "Fulong", family = "Yu", role = c("aut", "cre"), email = "fyu@broadinstitute.org", - comment = c(ORCID = "0000-0002-6100-8300")) + comment = c(ORCID = "0000-0002-6100-8300")), + person(given = "Brian", + family = "Schilder", + role = c("ctb"), + email = "brian_schilder@alumni.brown.edu", + comment = c(ORCID = "0000-0001-5949-2191")) + ) Description: SCAVENGE (Single Cell Analysis of Variant Enrichment through Network propagation of GEnomic data) optimizes the inference of functional and genetic associations to specific cells at single-cell resolution. License: GPL (>= 2) Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.2 +RoxygenNote: 7.2.3 Depends: R (>= 4.0.0) Imports: diff --git a/NEWS.md b/NEWS.md index 8f06baf..6b843dc 100644 --- a/NEWS.md +++ b/NEWS.md @@ -14,7 +14,7 @@ * New exported functions: - `example_data` * Add `example_results` as *data.R* -* Add runnable example for all exported functions. +* Add runnable examples for all exported functions. * Add *docker* vignette. ## Bug fixes diff --git a/README.Rmd b/README.Rmd index d9e5735..fd46968 100644 --- a/README.Rmd +++ b/README.Rmd @@ -1,5 +1,5 @@ --- -title: "" +title: "SCAVENGE" author: "`r rworkflows::use_badges()`" date: "

README updated: `r format( Sys.Date(), '%b-%d-%Y')`

" output: @@ -41,7 +41,6 @@ directly from GitHub by typing the following into an `R` console: ``` if(!require("remotes")) install.packages("remotes") - remotes::install_github("`r URL`") library(`r pkg`) ``` @@ -73,4 +72,4 @@ If you used or adapted SCAVENGE in your study, please cite our paper [[*Nat Biot ### Contact: If you run into issues and would like to report them, you can use the "Issues" tab on the left hand side. -Alternatively, you can contact authors: fyu{at}broadinstitute.org, lcato{at}broadinstitute.org and/or sankaran{at}broadinstitute.org. +Alternatively, you can contact authors: fyu{at}broadinstitute.org, lcato{at}broadinstitute.org and/or sankaran{at}broadinstitute.org. diff --git a/README.md b/README.md index 3ed7f04..10a7a33 100644 --- a/README.md +++ b/README.md @@ -1,18 +1,27 @@ -[![](https://img.shields.io/badge/devel%20version-1.0.2-black.svg)](https://github.com/sankaranlab/SCAVENGE) -[![R build -status](https://github.com/sankaranlab/SCAVENGE/workflows/rworkflows/badge.svg)](https://github.com/sankaranlab/SCAVENGE/actions) -[![](https://img.shields.io/github/last-commit/sankaranlab/SCAVENGE.svg)](https://github.com/sankaranlab/SCAVENGE/commits/master) -[![](https://img.shields.io/github/languages/code-size/sankaranlab/SCAVENGE.svg)](https://github.com/sankaranlab/SCAVENGE) -[![](https://app.codecov.io/gh/sankaranlab/SCAVENGE/branch/master/graph/badge.svg)](https://app.codecov.io/gh/sankaranlab/SCAVENGE) +SCAVENGE +================ [![License: GPL (\>= 2)](https://img.shields.io/badge/license-GPL%20(%3E=%202)-blue.svg)](https://cran.r-project.org/web/licenses/GPL%20(%3E=%202)) - -### SCAVENGE: Identifying genetic trait/phenotype relevant cell type/state at single cell resolution -

¶ Last updated: Dec-01-2022

+[![](https://img.shields.io/badge/devel%20version-1.0.2-black.svg)](https://github.com/sankaranlab/SCAVENGE) +[![](https://img.shields.io/github/languages/code-size/sankaranlab/SCAVENGE.svg)](https://github.com/sankaranlab/SCAVENGE) +[![](https://img.shields.io/github/last-commit/sankaranlab/SCAVENGE.svg)](https://github.com/sankaranlab/SCAVENGE/commits/master) +
[![R build +status](https://github.com/sankaranlab/SCAVENGE/workflows/rworkflows/badge.svg)](https://github.com/sankaranlab/SCAVENGE/actions) +[![](https://codecov.io/gh/sankaranlab/SCAVENGE/branch/master/graph/badge.svg)](https://codecov.io/gh/sankaranlab/SCAVENGE) +
+ +

+Authors: Fulong Yu, Brian Schilder +

+

+README updated: Mar-09-2023 +

+ +## `SCAVENGE`: Identifying genetic trait/phenotype relevant cell type/state at single cell resolution -### Overview +### Overview: Co-localization approaches using genetic variants and single-cell epigenomic data are unfortunately uninformative for many cells given the @@ -54,35 +63,34 @@ We welcome you to use SCAVENGE to discover more phenotype relevant cells! ### Installation: -The package -can be installed directly from GitHub by typing the following in an + +Once all of the dependencies for `SCAVENGE` are installed, the package +can be installed directly from GitHub by typing the following into an `R` console: -```R -if(!require("remotes")) install.packages("remotes") + if(!require("remotes")) install.packages("remotes") + remotes::install_github("https://github.com/sankaranlab/SCAVENGE") + library(SCAVENGE) -remotes::install_github("https://github.com/sankaranlab/SCAVENGE") -library(SCAVENGE) -``` +## Documentation -### Documentation - -### [Website](https://sankaranlab.github.io/SCAVENGE) -### [Getting started](https://sankaranlab.github.io/SCAVENGE/articles/SCAVENGE) -This web resource and vignette compiliation shows how to reproduce results of -SCAVENGE analysis with monocyte count on a 10X PBMC dataset. +### Tutorial: -### Tutorials +This web resource and vignette compiliation shows how to reproduce +results of SCAVENGE analysis with monocyte count on a 10X PBMC dataset +[\[**Vignette-pdf**\]](doc/SCAVENGE-vignette.pdf), [\[**Vignette-R +markdown code**\]](doc/SCAVENGE-vignette.Rmd). See the [\[**Wiki -page**\]](https://github.com/sankaranlab/SCAVENGE/wiki) for extra -information such as preparing your GWAS data for SCAVENGE (finemapping): -- [SCAVENGE] Preparing your GWAS data for finemapping -- [SCAVENGE] Preparing your scATAC-seq data -- [SCAVENGE] Rule of thumb of SCAVENGE analysis and intepretation -- [SCAVENGE-L] SCAVENGE-L method for single cell (mt)DNA mutation-based lineage tracing analysis +page**\]](https://github.com/sankaranlab/SCAVENGE/wiki) for some +information on preparing your GWAS data for SCAVENGE, including +finemapping. + +### [Website](https://sankaranlab.github.io/SCAVENGE) + +### [Getting started](https://sankaranlab.github.io/SCAVENGE/articles/SCAVENGE) -### FAQs +### FAQs: - *What input data are accepted for SCAVENGE analysis?* A: The count matrix of scATAC-seq data and fine-mapped variants from @@ -101,17 +109,18 @@ information such as preparing your GWAS data for SCAVENGE (finemapping): [\[**Discussions**\]](https://github.com/sankaranlab/SCAVENGE/discussions) page, please feel free to discuss and post your ideas. -### Citation +### Citation: If you used or adapted SCAVENGE in your study, please cite our paper [\[*Nat Biotechnol*\]](https://www.nature.com/articles/s41587-022-01341-y) \|\| [\[*PubMed*\]](https://pubmed.ncbi.nlm.nih.gov/35668323/). *Variant to function mapping at single-cell resolution through network -propagation.* - +propagation.* -### Contact -If you run into issues and would like to report them, you can submit an [Issue](https://github.com/sankaranlab/SCAVENGE/issues). -Alternatively, you can contact authors: fyu{at}broadinstitute.org, lcato{at}broadinstitute.org, cweng{at}wi.mit.edu, and/or sankaran{at}broadinstitute.org. +### Contact: +If you run into issues and would like to report them, you can use the +“Issues” tab on the left hand side. +Alternatively, you can contact authors: fyu{at}broadinstitute.org, +lcato{at}broadinstitute.org and/or sankaran{at}broadinstitute.org. diff --git a/inst/.DS_Store b/inst/.DS_Store deleted file mode 100644 index 10e1071..0000000 Binary files a/inst/.DS_Store and /dev/null differ diff --git a/man/.DS_Store b/man/.DS_Store deleted file mode 100644 index 5008ddf..0000000 Binary files a/man/.DS_Store and /dev/null differ diff --git a/vignettes/.DS_Store b/vignettes/.DS_Store deleted file mode 100644 index 4646921..0000000 Binary files a/vignettes/.DS_Store and /dev/null differ