theislab/scib: Benchmarking analysis of data integration tools - GitHub
Benchmarking atlas-level data integration in single-cell genomics. This repository contains the code for the scib package used in our benchmarking study for data integration tools. In our study, we benchmark 16 methods (see Tools) with 4 combinations of preprocessing steps leading to 68 methods combinations on 85 batches of gene expression and ...
Installation — scib 1.1.5 documentation - Read the Docs
The scib python package is available on PyPI and can be installed through. pip install scib. Alternatively, you can also install the package directly from GitHub directly via. pip install git+https://github.com/theislab/scib.git. Additionally, in order to run the R package kBET, you need to install it through R.
Benchmarking atlas-level data integration in single-cell genomics - Nature
Dec 23, 2021 · Single-cell integration benchmarking (scIB) We benchmarked 16 popular data integration methods on 13 preprocessed integration tasks: two simulation tasks, five...
Single-cell integration benchmark scib — scib 1.1.5 documentation
Benchmarking atlas-level data integration in single-cell genomics. This repository contains the code for the scib package used in our benchmarking study for data integration tools. In our study, we benchmark 16 methods (see Tools) with 4 combinations of preprocessing steps leading to 68 methods combinations on 85 batches of gene expression and ...
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scib：基于Python的生物信息学分析工具箱 - CSDN博客
Aug 24, 2024 · scib 是一个由 theislab 开发的开源项目，专注于提供一套强大的工具集，用于加速生物信息学中的数据处理、分析和可视化。 该项目利用 Python 的灵活性和强大的科学计算库（如 NumPy、Pandas 和 Scikit-learn），旨在简化从基因表达数据分析到细胞类型识别等复杂生物 ...
Single-cell integration benchmarking - Theislab
Single-cell integration benchmarking (scIB) is a project to assess the performance of scRNA-seq batch integration methods. We have used 14 metrics to evaluate 16 methods on 7 scRNA-seq (5 real and 2 simulated) and 6 scATAC-seq tasks.
探索单细胞基因组学数据集成的未来——推荐scib开源项目-CSDN …
May 25, 2024 · 通过scib，你可以轻松复现实验并应用到自己的数据中。 项目技术分析. scib利用了流行的scanpy库来实现其功能。它包括以下核心组件： 预处理模块（scib.preprocessing或scib.pp）：提供了正常化、缩放和基于批次的选择高变基因等功能。
科学网—scIB：单细胞数据融合基准框架 - 张俊鹏的博文
Feb 18, 2022 · 既然涉及选择单细胞数据融合方法，就涉及基准问题，在基准框架内需要对不同方法进行评估和打分。. 其中，scIB （single-cell integration benchmarking）就是这样的一类单细胞数据融合基准框架。. 图1 scIB数据融合基准框架. scIB选用16种流行单细胞数据融合工具，并且 ...
scib · PyPI
Apr 1, 2024 · We created the python package called scib that uses scanpy to streamline the integration of single-cell datasets and evaluate the results. The package contains several modules for preprocessing an anndata object, running integration methods and evaluating the resulting using a number of metrics.