Source: https://docs.nygen.io/CyteType/
Revision: 6ce97c558d4353ff1796056a86b1e6d8b42f4b4e
Structured page: https://docs.nygen.io/CyteType/index.json

CyteType

CyteType annotates the clusters of single-cell RNA-seq data. You provide the clusters and marker genes you have computed, from Python with Scanpy and AnnData or from R with Seurat, and CyteType returns for each cluster a cell type label, a Cell Ontology term, a cell state and a confidence rating from an independent review step. The annotation runs on CyteType’s servers, and an interactive report shows the evidence behind every label.

A first run

Install the client, sign in once, then annotate a clustered dataset. Using CyteType requires an API key: cytetype setup or SetupCyteTypeR() signs you in with your browser and saves your key on this computer.

Python

R

pip install cytetype
cytetype setup

import scanpy as sc
from cytetype import CyteType

# adata holds log-normalized expression and Leiden clusters in adata.obs["leiden"].
sc.tl.rank_genes_groups(adata, groupby="leiden", key_added="rank_genes_leiden")

annotator = CyteType(adata, group_key="leiden", rank_key="rank_genes_leiden")
adata = annotator.run(
    study_context="Peripheral blood mononuclear cells from a healthy human donor."
)

install.packages("devtools")
devtools::install_github("NygenAnalytics/CyteTypeR")
CyteTypeR::SetupCyteTypeR()

library(Seurat)
library(CyteTypeR)

# obj holds normalized data in its RNA assay, a UMAP and clusters from
# FindClusters().
markers <- FindAllMarkers(obj, only.pos = TRUE)
prepped <- PrepareCyteTypeR(obj, markers, group_key = "seurat_clusters")
obj <- CyteTypeR(
  obj,
  prepped,
  study_context = "Peripheral blood mononuclear cells from a healthy human donor."
)

The link to the report is printed as soon as the job starts. The Python quickstart <https://docs.nygen.io/CyteType/getting-started/quickstart> and the R quickstart <https://docs.nygen.io/CyteType/getting-started/quickstart-r> walk through a complete example.

Where to go next

Getting started: install the client <https://docs.nygen.io/CyteType/getting-started/installation>, sign in <https://docs.nygen.io/CyteType/getting-started/sign-in>, and read how CyteType works <https://docs.nygen.io/CyteType/getting-started/how-cytetype-works>.

Prepare and run: prepare your data <https://docs.nygen.io/CyteType/guides/prepare-data>, work with large datasets <https://docs.nygen.io/CyteType/guides/large-datasets>, write a study context <https://docs.nygen.io/CyteType/guides/study-context>, run, monitor and rerun jobs <https://docs.nygen.io/CyteType/guides/running-jobs>, use your own LLM <https://docs.nygen.io/CyteType/guides/llm-configuration>, and run CyteType from scripts, HPC and CI <https://docs.nygen.io/CyteType/guides/automation>.

Results: find the results in AnnData and Seurat <https://docs.nygen.io/CyteType/results/results-in-your-data>, read the CyteType report <https://docs.nygen.io/CyteType/results/report>, and interpret and review the results <https://docs.nygen.io/CyteType/results/interpreting-results>.

Platform: manage your jobs in the dashboard <https://docs.nygen.io/CyteType/platform/dashboard>, control visibility and sharing <https://docs.nygen.io/CyteType/platform/sharing>, ask questions about your results in Chat <https://docs.nygen.io/CyteType/platform/chat>, run a target analysis <https://docs.nygen.io/CyteType/platform/target-analysis>, connect AI assistants <https://docs.nygen.io/CyteType/platform/mcp> through MCP, and check the usage limits <https://docs.nygen.io/CyteType/platform/limits>.

Reference: the Python API <https://docs.nygen.io/CyteType/api/index.html>, the R functions <https://docs.nygen.io/CyteType/reference/r-api>, the command line <https://docs.nygen.io/CyteType/reference/cli> and the error codes <https://docs.nygen.io/CyteType/reference/errors>.

Support: troubleshooting <https://docs.nygen.io/CyteType/support/troubleshooting>, the FAQ <https://docs.nygen.io/CyteType/support/faq>, security and privacy <https://docs.nygen.io/CyteType/support/security-and-privacy> and how to cite CyteType <https://docs.nygen.io/CyteType/support/citing>.

Source code and issues

The Python client is developed in NygenAnalytics/CyteType <https://github.com/NygenAnalytics/CyteType> and the R package in NygenAnalytics/CyteTypeR <https://github.com/NygenAnalytics/CyteTypeR>. Report problems in the CyteType issues <https://github.com/NygenAnalytics/CyteType/issues> or the CyteTypeR issues <https://github.com/NygenAnalytics/CyteTypeR/issues>. The documentation index for LLMs <https://docs.nygen.io/CyteType/llms.txt> lists every page in plain text for assistants that read this site.