diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
new file mode 100644
index 0000000..875ae87
--- /dev/null
+++ b/.github/CONTRIBUTING.md
@@ -0,0 +1,288 @@
+# Contributing to SCWorkflow
+
+## Proposing changes with issues
+
+If you want to make a change, it's a good idea to first
+[open an issue](https://code-review.tidyverse.org/issues/)
+and make sure someone from the team agrees that it’s needed.
+
+If you've decided to work on an issue,
+[assign yourself to the issue](https://docs.github.com/en/issues/tracking-your-work-with-issues/assigning-issues-and-pull-requests-to-other-github-users#assigning-an-individual-issue-or-pull-request)
+so others will know you're working on it.
+
+## Pull request process
+
+We use [GitHub Flow](https://docs.github.com/en/get-started/using-github/github-flow)
+as our collaboration process.
+Follow the steps below for detailed instructions on contributing changes to
+SCWorkflow.
+
+
+
+
+### Clone the repo
+
+If you are a member of [CCBR](https://github.com/CCBR),
+you can clone this repository to your computer or development environment.
+Otherwise, you will first need to
+[fork](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo)
+the repo and clone your fork. You only need to do this step once.
+
+```sh
+git clone https://github.com/CCBR/SCWorkflow
+```
+
+> Cloning into 'SCWorkflow'...
+> remote: Enumerating objects: 1136, done.
+> remote: Counting objects: 100% (463/463), done.
+> remote: Compressing objects: 100% (357/357), done.
+> remote: Total 1136 (delta 149), reused 332 (delta 103), pack-reused 673
+> Receiving objects: 100% (1136/1136), 11.01 MiB | 9.76 MiB/s, done.
+> Resolving deltas: 100% (530/530), done.
+
+```sh
+cd SCWorkflow
+```
+
+### If this is your first time cloning the repo, install dependencies
+
+- In an R console, install the R development dependencies with
+ `devtools::install_dev_deps()`, and then make sure the package passes R CMD
+ check by running `devtools::check()`. If R CMD check doesn't pass cleanly,
+ it's a good idea to ask for help before continuing.
+
+- Install [`pre-commit`](https://pre-commit.com/#install) if you don't already
+ have it. Then from the repo's root directory, run
+
+ ```sh
+ pre-commit install
+ ```
+
+ This will install the repo's pre-commit hooks.
+ You'll only need to do this step the first time you clone the repo.
+
+### Create a branch
+
+ Create a Git branch for your pull request (PR). Give the branch a descriptive
+ name for the changes you will make, such as `iss-10` if it is for a specific
+ issue.
+
+ ```sh
+ # create a new branch and switch to it
+ git branch iss-10
+ git switch iss-10
+ ```
+
+ > Switched to a new branch 'iss-10'
+
+### Make your changes
+
+Edit the code, write unit tests, and update the documentation as needed.
+
+#### style
+
+New code should follow the [tidyverse style guide](https://style.tidyverse.org).
+You can use the [styler](https://CRAN.R-project.org/package=styler) package to
+apply these styles, but please don't restyle code that has nothing to do with
+your PR.
+
+A brief overview of conventions according to the tidyverse style guide:
+
+- most object names (variables and functions) should be in [snake_case](https://style.tidyverse.org/syntax.html#sec-objectnames)
+- function names should use [verbs](https://style.tidyverse.org/functions.html#naming) where possible
+- use `<-` for assignment
+- use [pipes](https://style.tidyverse.org/pipes.html) to chain operations on a single object
+
+Please see the [tidyverse style guide](https://style.tidyverse.org) for more details.
+
+#### test
+
+Most changes to the code will also need unit tests to demonstrate that the
+changes work as intended.
+Use [`testthat`](https://testthat.r-lib.org/) to create your unit tests and test
+the code.
+Test files are organized as described in
+.
+Take a look at the existing code in this package for examples.
+
+#### document
+
+If you have written a new function or changed the API of an existing function,
+you will need to update the function's documentation using
+[roxygen2](https://cran.r-project.org/package=roxygen2) with
+[Markdown syntax](https://roxygen2.r-lib.org/articles/rd-formatting.html).
+See instructions on writing roxygen2 comments here:
+.
+If the function is used in a vignette, you may also need to update the vignette.
+
+#### check
+
+After making your changes, run `devtools::check()` from an R console to make
+sure the package still passes R CMD check.
+
+### Commit and push your changes
+
+If you're not sure how often you should commit or what your commits should
+consist of, we recommend following the "atomic commits" principle where each
+commit contains one new feature, fix, or task.
+Learn more about atomic commits here:
+
+
+First, add the files that you changed to the staging area:
+
+```sh
+git add path/to/changed/files/
+```
+
+Then make the commit.
+Your commit message should follow the
+[Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0/)
+specification.
+Briefly, each commit should start with one of the approved types such as
+`feat`, `fix`, `docs`, etc. followed by a description of the commit.
+Take a look at the [Conventional Commits specification](https://www.conventionalcommits.org/en/v1.0.0/#summary)
+for more detailed information about how to write commit messages.
+
+
+```sh
+git commit -m 'feat: create function for awesome feature'
+```
+
+pre-commit will enforce that your commit message and the code changes are
+styled correctly and will attempt to make corrections if needed.
+
+> Check for added large files..............................................Passed
+> Fix End of Files.........................................................Passed
+> Trim Trailing Whitespace.................................................Failed
+> - hook id: trailing-whitespace
+> - exit code: 1
+> - files were modified by this hook
+>
+> Fixing path/to/changed/files/file.txt
+>
+> codespell................................................................Passed
+> style-files..........................................(no files to check)Skipped
+> readme-rmd-rendered..................................(no files to check)Skipped
+> use-tidy-description.................................(no files to check)Skipped
+
+In the example above, one of the hooks modified a file in the proposed commit,
+so the pre-commit check failed. You can run `git diff` to see the changes that
+pre-commit made and `git status` to see which files were modified. To proceed
+with the commit, re-add the modified file(s) and re-run the commit command:
+
+```sh
+git add path/to/changed/files/file.txt
+git commit -m 'feat: create function for awesome feature'
+```
+
+This time, all the hooks either passed or were skipped
+(e.g. hooks that only run on R code will not run if no R files were
+committed).
+When the pre-commit check is successful, the usual commit success message
+will appear after the pre-commit messages showing that the commit was created.
+
+> Check for added large files..............................................Passed
+> Fix End of Files.........................................................Passed
+> Trim Trailing Whitespace.................................................Passed
+> codespell................................................................Passed
+> style-files..........................................(no files to check)Skipped
+> readme-rmd-rendered..................................(no files to check)Skipped
+> use-tidy-description.................................(no files to check)Skipped
+> Conventional Commit......................................................Passed
+> [iss-10 9ff256e] feat: create function for awesome feature
+> 1 file changed, 22 insertions(+), 3 deletions(-)
+
+Finally, push your changes to GitHub:
+
+```sh
+git push
+```
+
+If this is the first time you are pushing this branch, you may have to
+explicitly set the upstream branch:
+
+```sh
+git push --set-upstream origin iss-10
+```
+
+> Enumerating objects: 7, done.
+> Counting objects: 100% (7/7), done.
+> Delta compression using up to 10 threads
+> Compressing objects: 100% (4/4), done.
+> Writing objects: 100% (4/4), 648 bytes | 648.00 KiB/s, done.
+> Total 4 (delta 3), reused 0 (delta 0), pack-reused 0
+> remote: Resolving deltas: 100% (3/3), completed with 3 local objects.
+> remote:
+> remote: Create a pull request for 'iss-10' on GitHub by visiting:
+> remote: https://github.com/CCBR/SCWorkflow/pull/new/iss-10
+> remote:
+> To https://github.com/CCBR/SCWorkflow
+>
+> [new branch] iss-10 -> iss-10
+> branch 'iss-10' set up to track 'origin/iss-10'.
+
+We recommend pushing your commits often so they will be backed up on GitHub.
+You can view the files in your branch on GitHub at
+`https://github.com/CCBR/SCWorkflow/tree/`
+(replace `` with the actual name of your branch).
+
+### Create the PR
+
+Once your branch is ready, create a PR on GitHub:
+
+
+Select the branch you just pushed:
+
+
+
+Edit the PR title and description.
+The title should briefly describe the change.
+Follow the comments in the template to fill out the body of the PR, and
+you can delete the comments (everything between ``) as you go.
+When you're ready, click 'Create pull request' to open it.
+
+
+
+Optionally, you can mark the PR as a draft if you're not yet ready for it to
+be reviewed, then change it later when you're ready.
+
+### Wait for a maintainer to review your PR
+
+We will do our best to follow the tidyverse code review principles:
+.
+The reviewer may suggest that you make changes before accepting your PR in
+order to improve the code quality or style.
+If that's the case, continue to make changes in your branch and push them to
+GitHub, and they will appear in the PR.
+
+Once the PR is approved, the maintainer will merge it and the issue(s) the PR
+links will close automatically.
+Congratulations and thank you for your contribution!
+
+### After your PR has been merged
+
+After your PR has been merged, update your local clone of the repo by
+switching to the main branch and pulling the latest changes:
+
+```sh
+git checkout main
+git pull
+```
+
+It's a good idea to run `git pull` before creating a new branch so it will
+start from the most recent commits in main.
+
+## Helpful links for more information
+
+- This contributing guide was adapted from the [tidyverse contributing guide](https://github.com/tidyverse/tidyverse/blob/main/.github/CONTRIBUTING.md)
+- [GitHub Flow](https://docs.github.com/en/get-started/using-github/github-flow)
+- [tidyverse style guide](https://style.tidyverse.org)
+- [tidyverse code review principles](https://code-review.tidyverse.org)
+- [reproducible examples](https://www.tidyverse.org/help/#reprex)
+- [R packages book](https://r-pkgs.org/)
+- packages:
+ - [usethis](https://usethis.r-lib.org/)
+ - [devtools](https://devtools.r-lib.org/)
+ - [testthat](https://testthat.r-lib.org/)
+ - [styler](https://styler.r-lib.org/)
+ - [roxygen2](https://roxygen2.r-lib.org)
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
new file mode 100644
index 0000000..95c98d1
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -0,0 +1,45 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+ - type: markdown
+ attributes:
+ value: |
+ Before you submit this issue, please check the documentation:
+
+ - type: textarea
+ id: description
+ attributes:
+ label: Description of the bug
+ description: A clear and concise description of what the bug is.
+ validations:
+ required: true
+
+ - type: textarea
+ id: reprex
+ attributes:
+ label: Code and output
+ description: Please include a minimal reproducible example (AKA a reprex). If you've never heard of a [reprex](http://reprex.tidyverse.org/) before, start by reading .
+ render: console
+ placeholder: |
+ library(SCWorkflow)
+ ... insert_your_code_here() ...
+
+ Paste some output where something broke
+
+ - type: textarea
+ id: files
+ attributes:
+ label: Relevant files
+ description: |
+ Please drag and drop any relevant files here if applicable. Create a `.zip` archive if the extension is not allowed.
+
+ - type: textarea
+ id: system
+ attributes:
+ label: System information
+ description: |
+ * Version of R
+ * Version of CCBR/SCWorkflow
+ * OS _(eg. Ubuntu Linux, macOS)_
+ * Hardware _(eg. HPC, Desktop)_
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
new file mode 100644
index 0000000..84f8757
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/config.yml
@@ -0,0 +1,4 @@
+contact_links:
+ - name: Discussions
+ url: https://github.com/CCBR/SCWorkflow/discussions
+ about: Please ask and answer questions here.
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
new file mode 100644
index 0000000..73a08f5
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -0,0 +1,11 @@
+name: Feature request
+description: Suggest an idea for the package
+labels: enhancement
+body:
+ - type: textarea
+ id: description
+ attributes:
+ label: Description of feature
+ description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+ validations:
+ required: true
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
new file mode 100644
index 0000000..bc679fa
--- /dev/null
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -0,0 +1,24 @@
+## Changes
+
+
+
+## Issues
+
+
+
+## PR Checklist
+
+(~Strikethrough~ any points that are not applicable.)
+
+- [ ] This comment contains a description of changes with justifications, with any relevant issues linked.
+- [ ] Write unit tests for any new features, bug fixes, or other code changes.
+- [ ] Update the docs if there are any API changes (roxygen2 comments, vignettes, readme, etc.).
+- [ ] Update `NEWS.md` with a short description of any user-facing changes and reference the PR number. Follow the style described in
+- [ ] Run `devtools::check()` locally and fix all notes, warnings, and errors.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
new file mode 100644
index 0000000..07d305f
--- /dev/null
+++ b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,118 @@
+# 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, dev, DEV]
+ pull_request:
+ branches: [main, master, dev, DEV]
+ workflow_dispatch:
+
+name: R-CMD-check
+
+permissions:
+ contents: read
+ pull-requests: read
+
+jobs:
+ R-CMD-check:
+ strategy:
+ fail-fast: false
+ matrix:
+ config:
+ - { os: ubuntu-latest, r: '4.1.3' }
+ #- { os: ubuntu-latest, r: 'oldrel-1' }
+ #- { os: macos-latest, r: 'release' }
+ runs-on: ${{ matrix.config.os }}
+ name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ R_KEEP_PKG_SOURCE: yes
+ container:
+ image: nciccbr/scworkflow:v1.0.2_79e5d37
+ steps:
+ - uses: actions/checkout@v4
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: local::.
+ needs: dev
+ - uses: r-lib/actions/check-r-package@v2
+ with:
+ upload-snapshots: true
+
+ lint:
+ runs-on: ubuntu-latest
+ container:
+ image: nciccbr/scworkflow:v1.0.2_79e5d37
+ steps:
+ - uses: actions/checkout@v4
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ needs: dev
+ - name: Good Practice checks
+ shell: Rscript {0}
+ run: |
+ g <- goodpractice::gp()
+ g
+ n_failed <- length(goodpractice::failed_checks(g))
+ if (n_failed > 0) {
+ warning(paste(n_failed, "failed checks"))
+ }
+ - name: Lint
+ shell: Rscript {0}
+ run: lintr::lint_package()
+ env:
+ LINTR_ERROR_ON_LINT: false
+
+ test-coverage:
+ runs-on: ubuntu-latest
+ container:
+ image: nciccbr/scworkflow:v1.0.2_79e5d37
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ steps:
+ - uses: actions/checkout@v4
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ needs: dev
+ - name: Test coverage
+ run: |
+ cov <- covr::package_coverage(
+ quiet = FALSE,
+ clean = FALSE,
+ install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+ )
+ covr::to_cobertura(cov)
+ shell: Rscript {0}
+ - uses: codecov/codecov-action@v4
+ with:
+ fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+ file: ./cobertura.xml
+ plugin: noop
+ disable_search: true
+ token: ${{ secrets.CODECOV_TOKEN }}
+ - name: Show testthat output
+ if: always()
+ run: |
+ ## --------------------------------------------------------------------
+ find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+ shell: bash
+ - name: Upload test results
+ if: failure()
+ uses: actions/upload-artifact@v4
+ with:
+ name: coverage-test-failures
+ path: ${{ runner.temp }}/package
+
+ check: # make sure all check jobs pass. https://github.com/orgs/community/discussions/4324#discussioncomment-3477871
+ runs-on: ubuntu-latest
+ container:
+ image: nciccbr/scworkflow:v1.0.2_79e5d37
+ needs: [R-CMD-check, lint, test-coverage]
+ if: always()
+ steps:
+ - name: Successful build
+ if: ${{ !(contains(needs.*.result, 'failure')) }}
+ run: exit 0
+ - name: Failing build
+ if: ${{ contains(needs.*.result, 'failure') }}
+ run: exit 1
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index f9745ba..e5b2def 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -2,7 +2,7 @@
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
push:
- branches: [main, master, GalaxyCLI]
+ branches: [main, master]
pull_request:
branches: [main, master]
release:
@@ -23,20 +23,15 @@ jobs:
group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ container:
+ image: nciccbr/scworkflow:v1.0.2_79e5d37
steps:
- uses: actions/checkout@v3
- - uses: r-lib/actions/setup-pandoc@v2
-
- - uses: r-lib/actions/setup-r@v2
- with:
- use-public-rspm: true
- r-version: 4.3
-
- uses: r-lib/actions/setup-r-dependencies@v2
with:
- extra-packages: any::pkgdown, local::.
- needs: website
+ extra-packages: local::.
+ needs: dev
- name: Build site
run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
diff --git a/.github/workflows/user-projects.yml b/.github/workflows/user-projects.yml
new file mode 100644
index 0000000..c189ef6
--- /dev/null
+++ b/.github/workflows/user-projects.yml
@@ -0,0 +1,23 @@
+name: user-projects
+
+on:
+ issues:
+ types:
+ - assigned
+ pull_request:
+ types:
+ - assigned
+
+permissions:
+ issues: write
+ pull-requests: write
+
+jobs:
+ add-to-project:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: CCBR/actions/user-projects@main
+ with:
+ app-id: ${{ vars.CCBR_BOT_APP_ID }}
+ app-private-key: ${{ secrets.CCBR_BOT_PRIVATE_KEY }}
+ token-owner: "CCBR"
diff --git a/.gitignore b/.gitignore
index 55ed9b9..17be9e8 100755
--- a/.gitignore
+++ b/.gitignore
@@ -5,4 +5,3 @@ Rcheck.txt
*.pdf
tests/testthat/otherData/
.Rproj.user
-*.txt
diff --git a/DESCRIPTION b/DESCRIPTION
index cdf6c35..3bbcff8 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,89 +1,103 @@
Package: SCWorkflow
Title: SCWorkflow from NIDAP
Version: 1.0.2
-Authors@R: c(person("Maggie", "Cam", email = "maggie.cam@nih.gov", role = "aut", comment = c(ORCID = "0000-0001-8190-9766")),
- person("Thomas", "Meyer", email = "thomas.meyer@nih.gov", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7185-5597")),
- person("Jing", "Bian", email = "bianjh@nih.gov", role = "aut", comment = c(ORCID = "0000-0001-7109-716X")),
- person("Alexandra", "Michalowski", email = "michaloa@mail.nih.gov", role = "aut", comment = c(ORCID = "0000-0001-9259-6101")),
- person("Alexei", "Lobanov", email = "alexei.lobanov@nih.gov", role = "aut", comment = c(ORCID = "0000-0002-9883-4374")),
- person("Philip", "Homan", email = "philip.homan@nih.gov", role = "aut", comment = c(ORCID = "0000-0002-3389-4931")),
- person("Rui", "He", email = "rui.he@nih.gov", role = "aut"))
-Description: A set of functions for analyzing single-cell RNA-seq data using the
- Seurat workflow. The user provides H5 files containing the results of the
- upstream processing through CellRanger, and the package functions allow for
- the QC, filtering, normalization, annotation, differential gene expression,
- and further visualizations and analysis based on user input. This package can
- be run both in a docker container and in user-friendly web-based interactive
- notebooks (NIDAP, Palantir Foundry).
+Authors@R: c(
+ person("Maggie", "Cam", , "maggie.cam@nih.gov", role = "aut",
+ comment = c(ORCID = "0000-0001-8190-9766")),
+ person("Thomas", "Meyer", , "thomas.meyer@nih.gov", role = c("aut", "cre"),
+ comment = c(ORCID = "0000-0002-7185-5597")),
+ person("Jing", "Bian", , "bianjh@nih.gov", role = "aut",
+ comment = c(ORCID = "0000-0001-7109-716X")),
+ person("Alexandra", "Michalowski", , "michaloa@mail.nih.gov", role = "aut",
+ comment = c(ORCID = "0000-0001-9259-6101")),
+ person("Alexei", "Lobanov", , "alexei.lobanov@nih.gov", role = "aut",
+ comment = c(ORCID = "0000-0002-9883-4374")),
+ person("Philip", "Homan", , "philip.homan@nih.gov", role = "aut",
+ comment = c(ORCID = "0000-0002-3389-4931")),
+ person("Rui", "He", , "rui.he@nih.gov", role = "aut")
+ )
+Description: A set of functions for analyzing single-cell RNA-seq data
+ using the Seurat workflow. The user provides H5 files containing the
+ results of the upstream processing through CellRanger, and the package
+ functions allow for the QC, filtering, normalization, annotation,
+ differential gene expression, and further visualizations and analysis
+ based on user input. This package can be run both in a docker
+ container and in user-friendly web-based interactive notebooks (NIDAP,
+ Palantir Foundry).
License: MIT
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
-Suggests:
- testthat (>= 3.0.0)
Depends:
R (>= 4.0)
Imports:
anndata (>= 0.7.5.2),
+ BiocManager,
callr (>= 3.7.1),
+ celldex,
+ colorspace,
+ ComplexHeatmap (>= 2.10.0),
cowplot (>= 1.1.1),
data.table (>= 1.14.2),
+ dendextend,
+ dendsort,
+ digest (>= 0.6.29),
dplyr (>= 1.0.9),
edgeR (>= 3.36.0),
- future.apply (>= 1.9.0),
future (>= 1.27.0),
+ future.apply (>= 1.9.0),
gargle (>= 1.2.0),
+ gdata,
+ ggExtra,
ggplot2 (>= 3.3.6),
ggpubr (>= 0.4.0),
+ ggrepel,
globals (>= 0.16.1),
+ gridBase (>= 0.4-7),
+ gridExtra (>= 2.3),
+ gtable (>= 0.3.1),
harmony (>= 0.1.1),
hdf5r (>= 1.3.5),
+ htmlwidgets,
httpuv (>= 1.6.5),
+ httr,
+ jsonlite,
leiden (>= 0.4.2),
limma (>= 3.50.3),
magrittr (>= 2.0.3),
markdown (>= 1.1),
+ MAST (>= 1.20.0),
methods (>= 4.1.3),
- plotly (>= 4.10.0),
+ pheatmap,
+ plotly (>= 4.10.0),
+ plyr,
+ png,
progressr (>= 0.10.1),
- pryr (>= 0.1.5),
purrr (>= 0.3.4),
quantmod (>= 0.4.20),
+ RColorBrewer (>= 1.1-3),
reshape2 (>= 1.4.4),
reticulate (>= 1.25),
rlang (>= 1.0.6),
+ scales,
+ scDblFinder,
+ Seurat (>= 4.1.1),
+ SingleR (>= 1.8.1),
statmod (>= 1.4.37),
stringr (>= 1.4.1),
svglite (>= 2.1.0),
tibble (>= 3.1.8),
+ tidyr,
tidyverse (>= 1.3.2),
viridisLite (>= 0.4.0),
xfun (>= 0.32),
- zip (>= 2.2.0),
- ComplexHeatmap (>= 2.10.0),
- MAST (>= 1.20.0),
- SingleR (>= 1.8.1),
- BiocManager,
- gridBase (>= 0.4-7),
- gridExtra (>= 2.3),
- RColorBrewer (>= 1.1-3),
- Seurat (>= 4.1.1),
- gtable (>= 0.3.1),
- digest (>= 0.6.29),
- png,
- ggExtra,
- httr,
- jsonlite,
- plyr,
- colorspace,
- dendextend,
- dendsort,
- pheatmap,
- scales,
- celldex,
- gdata,
- ggrepel,
- tidyr,
- htmlwidgets,
- scDblFinder
+ zip (>= 2.2.0)
+Suggests:
+ knitr,
+ rmarkdown,
+ roxygen2,
+ testthat (>= 3.0.0),
+ usethis
+Config/Needs/dev: cffr, covr, goodpractice, here, lintr, pkgdown,
+ rcmdcheck
Config/testthat/edition: 3
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
diff --git a/Dockerfile b/Dockerfile
index b91c92f..0d61765 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -8,7 +8,7 @@ ENV BUILD_TAG=${BUILD_TAG}
ARG REPONAME="000000"
ENV REPONAME=${REPONAME}
-ARG R_VERSION=4.3.2
+ARG R_VERSION=4.1.3
ENV R_VERSION=${R_VERSION}
SHELL ["/bin/bash", "-lc"]