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| Original file line number | Diff line number | Diff line change |
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| @@ -1,4 +1,3 @@ | ||
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| # scdrake | ||
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| [](h | |
| CI](https://github.com/bioinfocz/scdrake/actions/workflows/docker-ci.yml/badge.svg?branch=main)](https://github.com/bioinfocz/scdrake/actions/workflows/docker-ci.yml) | ||
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| `{scdrake}` is a scalable and reproducible pipeline for secondary | ||
| analysis of droplet-based single-cell RNA-seq data. `{scdrake}` is an R | ||
| analysis of droplet-based single-cell RNA-seq data (scRNA-seq) and | ||
| spot-based spatial transcriptomics data (SRT). `{scdrake}` is an R | ||
| package built on top of the `{drake}` package, a | ||
| [Make](https://www.gnu.org/software/make)-like pipeline toolkit for [R | ||
| language](https://www.r-project.org). | ||
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@@ -28,11 +28,17 @@ The main features of the `{scdrake}` pipeline are: | |
| - Import of scRNA-seq data: [10x Genomics Cell | ||
| Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) | ||
| output, delimited table, or `SingleCellExperiment` object. | ||
| - Quality control and filtering of cells and genes, removal of empty | ||
| droplets. | ||
| - Import of SRT data: [10x Genomics Space | ||
| Ranger](https://www.10xgenomics.com/support/software/space-ranger/latest/getting-started/what-is-space-ranger) | ||
| output, delimited table, or `SingleCellExperiment` object, and | ||
| tissue positions file as in Space ranger. | ||
| - Quality control and filtering of cells/spots and genes, removal of | ||
| empty droplets. | ||
| - Higly variable genes detection, cell cycle scoring, normalization, | ||
| clustering, and dimensionality reduction. | ||
| - Cell type annotation. | ||
| - Spatially variable genes detection (for SRT data) | ||
| - Cell type annotation using reference sets, cell type annotation | ||
| using user-provided marker genes. | ||
| - Integration of multiple datasets. | ||
| - Computation of cluster markers and differentially expressed genes | ||
| between clusters (denoted as “contrasts”). | ||
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@@ -107,27 +113,21 @@ you can use `singularity pull docker-daemon:<image>` | |
| You can pull the Docker image with the latest stable `{scdrake}` version | ||
| using | ||
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| ``` bash | ||
| docker pull jirinovo/scdrake:1.5.2 | ||
| singularity pull docker:jirinovo/scdrake:1.5.2 | ||
| ``` | ||
| docker pull jirinovo/scdrake:1.5.2 | ||
| singularity pull docker:jirinovo/scdrake:1.5.2 | ||
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| or list available versions in [our Docker Hub | ||
| repository](https://hub.docker.com/r/jirinovo/scdrake/tags). | ||
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| For the latest development version use | ||
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| ``` bash | ||
| docker pull jirinovo/scdrake:latest | ||
| singularity pull docker:jirinovo/scdrake:latest | ||
| ``` | ||
| docker pull jirinovo/scdrake:latest | ||
| singularity pull docker:jirinovo/scdrake:latest | ||
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| **Note for Mac users with M1/M2 chipsets**: until version 1.5.0 | ||
| (inclusive), `arm64` images are available. | ||
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| ``` bash | ||
| docker pull jirinovo/scdrake:1.5.0-bioc3.15-arm64 | ||
| ``` | ||
| docker pull jirinovo/scdrake:1.5.0-bioc3.15-arm64 | ||
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| ### Running the container | ||
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@@ -136,39 +136,33 @@ and Windows or MacOS running Docker Desktop. | |
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| First make a shared directory that will be mounted to the container: | ||
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| ``` bash | ||
| mkdir ~/scdrake_projects | ||
| cd ~/scdrake_projects | ||
| ``` | ||
| mkdir ~/scdrake_projects | ||
| cd ~/scdrake_projects | ||
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| And run the image that will expose RStudio Server on port 8787 on your | ||
| host: | ||
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| ``` bash | ||
| docker run -d \ | ||
| -v $(pwd):/home/rstudio/scdrake_projects \ | ||
| -p 8787:8787 \ | ||
| -e USERID=$(id -u) \ | ||
| -e GROUPID=$(id -g) \ | ||
| -e PASSWORD=1234 \ | ||
| jirinovo/scdrake:1.5.2 | ||
| ``` | ||
| docker run -d \ | ||
| -v $(pwd):/home/rstudio/scdrake_projects \ | ||
| -p 8787:8787 \ | ||
| -e USERID=$(id -u) \ | ||
| -e GROUPID=$(id -g) \ | ||
| -e PASSWORD=1234 \ | ||
| jirinovo/scdrake:1.5.2 | ||
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| For Singularity, also make shared directories and execute the container | ||
| (“run and forget”): | ||
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| ``` bash | ||
| mkdir -p ~/scdrake_singularity | ||
| cd ~/scdrake_singularity | ||
| mkdir -p home/${USER} scdrake_projects | ||
| singularity exec \ | ||
| -e \ | ||
| --no-home \ | ||
| --bind "home/${USER}/:/home/${USER},scdrake_projects/:/home/${USER}/scdrake_projects" \ | ||
| --pwd "/home/${USER}/scdrake_projects" \ | ||
| path/to/scdrake_image.sif \ | ||
| scdrake <args> <command> | ||
| ``` | ||
| mkdir -p ~/scdrake_singularity | ||
| cd ~/scdrake_singularity | ||
| mkdir -p home/${USER} scdrake_projects | ||
| singularity exec \ | ||
| -e \ | ||
| --no-home \ | ||
| --bind "home/${USER}/:/home/${USER},scdrake_projects/:/home/${USER}/scdrake_projects" \ | ||
| --pwd "/home/${USER}/scdrake_projects" \ | ||
| path/to/scdrake_image.sif \ | ||
| scdrake <args> <command> | ||
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| ## Installing `{scdrake}` manually (not recommended) | ||
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@@ -184,7 +178,7 @@ Click for details | |
| - For MacOS: | ||
| `$ brew install libxml2 imagemagick@6 harfbuzz fribidi libgit2 geos pandoc` | ||
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| ### Install R \>= 4.2 | ||
| ### Install R >= 4.2 | ||
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| See <https://cloud.r-project.org/> | ||
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@@ -197,79 +191,63 @@ management of local R libraries. It is intended to be used on a | |
| per-project basis, i.e. each project should use its own library of R | ||
| packages. | ||
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| ``` r | ||
| install.packages("renv") | ||
| ``` | ||
| install.packages("renv") | ||
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| ### Initialize a new `{renv}` library | ||
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| Switch to directory where you will analyze data and initialize a new | ||
| `{renv}` library: | ||
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| ``` r | ||
| renv::consent(TRUE) | ||
| renv::init() | ||
| ``` | ||
| renv::consent(TRUE) | ||
| renv::init() | ||
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| Now exit and run again R. You should see a message that renv library has | ||
| been activated. | ||
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| ### Install BiocManager | ||
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| ``` r | ||
| renv::install("BiocManager") | ||
| ``` | ||
| renv::install("BiocManager") | ||
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| ### Install Bioconductor 3.15 | ||
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| ``` r | ||
| BiocManager::install(version = "3.15") | ||
| ``` | ||
| BiocManager::install(version = "3.15") | ||
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| ### Restore `{scdrake}` dependencies from lockfile | ||
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| `{renv}` also allows to export the current installed versions of R | ||
| packages (and other things) into a lockfile. Such lockfile is available | ||
| for `{scdrake}` and you can use it to install all dependencies by | ||
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| ``` r | ||
| ## -- This is a lockfile for the latest stable version of scdrake. | ||
| download.file("https://raw.githubusercontent.com/bioinfocz/scdrake/1.5.2/renv.lock") | ||
| ## -- You can increase the number of CPU cores to speed up the installation. | ||
| options(Ncpus = 2) | ||
| renv::restore(lockfile = "renv.lock", repos = BiocManager::repositories()) | ||
| ``` | ||
| ## -- This is a lockfile for the latest stable version of scdrake. | ||
| download.file("https://raw.githubusercontent.com/bioinfocz/scdrake/1.5.2/renv.lock") | ||
| ## -- You can increase the number of CPU cores to speed up the installation. | ||
| options(Ncpus = 2) | ||
| renv::restore(lockfile = "renv.lock", repos = BiocManager::repositories()) | ||
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| For the lockfile for the latest development version use | ||
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| ``` r | ||
| download.file("https://raw.githubusercontent.com/bioinfocz/scdrake/main/renv.lock") | ||
| ``` | ||
| download.file("https://raw.githubusercontent.com/bioinfocz/scdrake/main/renv.lock") | ||
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| ### Install the `{scdrake}` package | ||
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| Now we can finally install the `{scdrake}` package, but using a | ||
| non-standard approach - without its dependencies (which are already | ||
| installed from the lockfile). | ||
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| ``` r | ||
| remotes::install_github( | ||
| "bioinfocz/[email protected]", | ||
| dependencies = FALSE, upgrade = FALSE, | ||
| keep_source = TRUE, build_vignettes = TRUE, | ||
| repos = BiocManager::repositories() | ||
| ) | ||
| ``` | ||
| remotes::install_github( | ||
| "bioinfocz/[email protected]", | ||
| dependencies = FALSE, upgrade = FALSE, | ||
| keep_source = TRUE, build_vignettes = TRUE, | ||
| repos = BiocManager::repositories() | ||
| ) | ||
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| For the latest development version use `"bioinfocz/scdrake"`. | ||
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| ### Install the command line interface (CLI) | ||
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| Optionally, you can install `{scdrake}`’s CLI scripts with | ||
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| ``` r | ||
| scdrake::install_cli() | ||
| ``` | ||
| scdrake::install_cli() | ||
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| CLI should be now accessible as a `scdrake` command. By default, the CLI | ||
| is installed into `~/.local/bin`, which is usually present in the `PATH` | ||
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@@ -341,28 +319,30 @@ website of the current development version. | |
| - General information: | ||
| - Pipeline overview: `vignette("pipeline_overview")` | ||
| - FAQ & Howtos: `vignette("scdrake_faq")` | ||
| - Spatial extention: `vignette("scdrake_spatial")` | ||
| - Command line interface (CLI): `vignette("scdrake_cli")` | ||
| - Config files (internals): `vignette("scdrake_config")` | ||
| - Environment variables: `vignette("scdrake_envvars")` | ||
| - General configs: | ||
| - Pipeline config -\> `vignette("config_pipeline")` | ||
| - Main config -\> `vignette("config_main")` | ||
| - Pipeline config -> `vignette("config_pipeline")` | ||
| - Main config -> `vignette("config_main")` | ||
| - Pipelines and stages: | ||
| - Single-sample pipeline: | ||
| - Stage `01_input_qc`: reading in data, filtering, quality | ||
| control -\> `vignette("stage_input_qc")` | ||
| control -> `vignette("stage_input_qc")` | ||
| - Stage `02_norm_clustering`: normalization, HVG selection, | ||
| dimensionality reduction, clustering, cell type annotation | ||
| -\> `vignette("stage_norm_clustering")` | ||
| SVG selection, dimensionality reduction, clustering, | ||
| (manual) cell type annotation -> | ||
| `vignette("stage_norm_clustering")` | ||
| - Integration pipeline: | ||
| - Stage `01_integration`: reading in data and integration -\> | ||
| `vignette("stage_integration")` | ||
| - Stage `01_integration`: reading in data and integration | ||
| -> `vignette("stage_integration")` | ||
| - Stage `02_int_clustering`: post-integration clustering and | ||
| cell annotation -\> `vignette("stage_int_clustering")` | ||
| cell annotation -> `vignette("stage_int_clustering")` | ||
| - Common stages: | ||
| - Stage `cluster_markers` -\> | ||
| - Stage `cluster_markers` -> | ||
| `vignette("stage_cluster_markers")` | ||
| - Stage `contrasts` (differential expression) -\> | ||
| - Stage `contrasts` (differential expression) -> | ||
| `vignette("stage_contrasts")` | ||
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| We encourage all users to read | ||
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@@ -384,9 +364,7 @@ Below is the citation output from using `citation("scdrake")` in R. | |
| Please run this yourself to check for any updates on how to cite | ||
| **scdrake**. | ||
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| ``` r | ||
| print(citation("scdrake"), bibtex = TRUE) | ||
| ``` | ||
| print(citation("scdrake"), bibtex = TRUE) | ||
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| To cite package ‘scdrake’ in publications use: | ||
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@@ -422,7 +400,7 @@ but if you need e.g. a general help. | |
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| If you want to contribute to `{scdrake}`, read the [contribution | ||
| guide](.github/CONTRIBUTING.md), please. All pull requests are welcome! | ||
| :slightly_smiling_face: | ||
| :slightly\_smiling\_face: | ||
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| ## Code of Conduct | ||
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@@ -436,8 +414,8 @@ contributing to this project, you agree to abide by its terms. | |
| ### Funding | ||
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| This work was supported by [ELIXIR CZ](https://www.elixir-czech.cz) | ||
| research infrastructure project (MEYS Grant No: LM2018131) including | ||
| access to computing and storage facilities. | ||
| research infrastructure project (MEYS Grant No: LM2018131 and LM2023055) | ||
| including access to computing and storage facilities. | ||
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| ### Software and methods used by `{scdrake}` | ||
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