Source: https://docs.nygen.io/CyteType/getting-started/installation/ Revision: 6ce97c558d4353ff1796056a86b1e6d8b42f4b4e Structured page: https://docs.nygen.io/CyteType/getting-started.installation.json Installation CyteType has two clients: cytetype, the Python package, for AnnData and Scanpy workflows; CyteTypeR, the R package, for Seurat workflows. Both prepare your data on your own computer and send it to the CyteType service at https://cytetype.nygen.io, where the annotation runs. Install the client for the environment you analyze your data in. You can install both; they share the same sign-in. Requirements Python R Language version Python 3.12 or newer R 4.2 or newer (see R notes ) Package source PyPI GitHub, with dependencies from CRAN and Bioconductor Single-cell toolkit AnnData, installed with cytetype Seurat, installed with CyteTypeR You also need internet access to https://cytetype.nygen.io and a CyteType account, which needs an institutional email address (see Sign in and API keys ). Install the client Python R With pip, in the virtual environment or conda environment you use for your analysis: pip install cytetype With uv: # Add CyteType to a uv project uv add cytetype # Or install it into the active virtual environment uv pip install cytetype The package also installs the cytetype command, which you use to sign in. With devtools, as in the CyteTypeR README: install.packages("devtools") devtools::install_github("NygenAnalytics/CyteTypeR") Or with pak: install.packages("pak") pak::pak("NygenAnalytics/CyteTypeR") Both installers also install the packages that CyteTypeR requires, including Seurat, duckdb and the Bioconductor package rhdf5 (see R notes ). Python notes Check your Python version first with python --version. pip only offers releases that support the Python you run it with. On Python 3.11, pip install cytetype installs release 0.12.0, the last one for 3.11, without any error. On older versions it finds no release at all. Prefer a dedicated environment. cytetype requires narrow version ranges of some common packages (anndata 0.12.x, pydantic 2.12.x and requests 2.32.x), so installing it into an existing environment can upgrade or downgrade them. R notes R 4.2 or newer. CyteTypeR requires it, and so does the duckdb package it uses. Check your version with R.version.string, and update R first if it is older. duckdb writes the cell metadata file that is uploaded with each job, and both installers add it for you. On Linux, CRAN installs duckdb from source, which can take a while. rhdf5 from Bioconductor. CyteTypeR writes the expression file with rhdf5, a Bioconductor package, and both installers add it for you. pak installs it from the Bioconductor repositories, which provide binary packages for Windows and macOS. devtools looks it up on Bioconductor’s Git server instead, which needs Git (or the git2r package) on your computer, and when it installs rhdf5 it builds it from source, which needs a compiler (Rtools on Windows, the Xcode Command Line Tools on macOS). If you do not have these tools, use pak. If rhdf5 fails to build with devtools, install it from Bioconductor first and tell devtools to keep it: install.packages("BiocManager") BiocManager::install("rhdf5") # Keep the installed rhdf5 instead of rebuilding it devtools::install_github("NygenAnalytics/CyteTypeR", upgrade = "never") Seurat and the other dependencies, such as SeuratObject and withr, are installed from CRAN when they are missing, so the first installation can take some time. Optional packages that CyteTypeR uses when they are installed (the installers do not add them): Package What it is for furrr and progressr With furrr, CyteTypeR uploads large files in parallel chunks (up to upload_max_workers, 6 by default); with the default show_progress = TRUE it also needs progressr. Without them, chunks are uploaded one at a time. Install the packages for the quickstart The quickstarts use the standard Scanpy and Seurat workflows to cluster the example data before annotating it. Python R Scanpy is not installed with cytetype. Install it with the leiden extra: pip install "scanpy[leiden]" # or, with uv uv add "scanpy[leiden]" The extra installs igraph and leidenalg, the two Leiden implementations Scanpy can use; the quickstart’s sc.tl.leiden(flavor="igraph") needs igraph. CyteType’s plotting helper, cytetype.marker_dotplot(), also needs Scanpy. The R quickstart uses Seurat and dplyr, which are installed with CyteTypeR. No other packages are needed. Check the installation Python R cytetype --version python -c "import cytetype; print(cytetype.__version__)" Both print the installed version, for example cytetype 0.21.0 and 0.21.0. If your shell cannot find the cytetype command, the environment’s scripts folder is not on your PATH. Activate the environment, or run the command through Python instead, for example python -m cytetype.cli --version. packageVersion("CyteTypeR") #> [1] '0.6.0' Update Python R pip install -U cytetype # or, with uv in a virtual environment uv pip install -U cytetype # or, with uv in a project uv lock --upgrade-package cytetype uv sync When Python imports cytetype, and when you run the cytetype command, the package asks PyPI for the latest version, waiting at most 2 seconds. If a newer release exists, it prints a warning such as: ⚠️ A newer CyteType version is available on PyPI ( -> ). Run `pip install -U cytetype` to update. The check stays silent when you are offline or PyPI cannot be reached. devtools::install_github("NygenAnalytics/CyteTypeR", force = TRUE) # or, with pak pak::pak("NygenAnalytics/CyteTypeR") force = TRUE reinstalls the package even if devtools thinks it is up to date. When you load the package with library(CyteTypeR), it asks GitHub for the latest CyteTypeR release, waiting at most 2 seconds. If a newer release exists, it prints a startup message such as: A newer version of CyteTypeR is available ( -> ). Run devtools::install_github('NygenAnalytics/CyteTypeR') to update. The check stays silent when you are offline or GitHub cannot be reached. After updating, restart your Python kernel or R session so that the new version is loaded. Optional: the cytetyper command for R Python users get the cytetype terminal command with the package. R users can install an equivalent command, cytetyper, which runs the CyteTypeR sign-in functions from a terminal: library(CyteTypeR) InstallCyteTypeRCli() The function prints and returns the path of the installed command. cytetyper has the same commands as the Python cytetype command: cytetyper setup # sign in with your browser (also: cytetyper get-key) cytetyper login # save an existing API key cytetyper logout # remove the saved key from this computer cytetyper dashboard # open the dashboard cytetyper view # open the report of a job cytetyper --version cytetyper only signs you in and opens pages. Annotation jobs always run from an R session with CyteTypeR(). You do not need the command at all: the R functions SetupCyteTypeR(), LoginCyteTypeR() and LogoutCyteTypeR() do the same things. Before you rely on it, check these points: It must stay next to Rscript. The command runs the Rscript in its own folder, so InstallCyteTypeRCli() copies it into the folder of the first Rscript on your R session’s PATH, after following symbolic links (with Homebrew or the CRAN installer for macOS, that is R’s own program folder). Keep the default destination; a copy in a folder without Rscript does not work. If you have several R versions, check that this Rscript belongs to the R where CyteTypeR is installed. If the function stops with Could not locate Rscript on PATH, add R’s bin folder to PATH and try again. That folder must be on your PATH. Otherwise a new terminal cannot find cytetyper. With the R installers from CRAN for macOS and Windows, R’s own program folder is usually not on PATH: add it, or run the command with the full path that InstallCyteTypeRCli() printed. On Windows the installed file is cytetyper.cmd. A system-wide R may need administrator rights. If you cannot write to R’s program folder, the function stops with Could not install cytetyper in . Check that the directory is writable. Ask your administrator, or use the R functions instead. It ignores your R startup files. The command starts R with --vanilla, which skips .Rprofile and .Renviron. If CyteTypeR is installed in a project library (for example with renv) or in a library that only those files point to, the command fails with Error: Unable to load CyteTypeR. Reinstall it for a new R version. A new R installation has its own program folder; run InstallCyteTypeRCli() again from the new version. Use overwrite = TRUE to replace an existing copy. Next step Sign in once on each computer you run CyteType from: Sign in and API keys . If the installation fails, see Troubleshooting .