{"repo":"yxwucq/scExtract","free":true,"listed":false,"github":"https://github.com/yxwucq/scExtract","clone":"git clone https://github.com/yxwucq/scExtract.git","description":"Automatic annotation of single-cell RNA-seq data from the literature","language":"Python","stars":48,"topics":["data-integration","large-language-models","python","scrna-seq"],"license":"BSD-2-Clause","category":"data-pipelines","readme_excerpt":"scExtract: Automatic annotation and integration of single-cell RNA-seq datasets from the literature scExtract is a tool for automating the extraction, processing, and annotation of single-cell data from literature. The tool is designed to use LLMs to extract relevant information from scientific articles and process the data. The input of the program are an anndata object and a PDF/txt file containing the article from which the single-cell data is to be extracted. Usage - Step1: Clone repo from github and install locally - Step2: run scExtract init to generate config file If you want to benchmark auto-annotation using similarity of annotated-text or later integrate your datasets, you need convert annotation to embedding using LLM, by setting CONVERT EMBEDDING = true . If you using GPTs for text extraction, you can set API STYLES = same to use same setting. But there are no official text-to-embedding model in Claudes, you can set API STYLES = azure openai and according api key and endpoint to use Openai t2e model while using Claudes for text extraction. - Finally, directly excute by typing scExtract : Annotate Using auto extract subcommand. Make sure to add Batch key to raw adata.obs for possible batch correction within dataset. Sample datasets can be found at https://zenodo.org/records/13827072. Integration For integration with standard scExtract pipeline, first install cellhint prior and scanorama prior. Then using integrate subcommand. For large dataset computed on HPC witho","default_branch":null,"files":null,"tree":[],"storefront":"/r/yxwucq","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/yxwucq/scExtract/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}