Soybean Expression Atlas v2

<strong>Overview</strong> This directory contains important files created during the construction of the Soybean Expression Atlas v2. <br> <strong>Directory structure</strong> Here, you can find the following files: <br> - `se_atlas_gene.rda`: A *SummarizedExperiment* object containing gene-level transcript abundances in TPM and bias-corrected counts, which are stored in the `gene_TPM` and `gene_counts` assays, respectively. <br> - `se_atlas_transcript.rda`: A *SummarizedExperiment* object containing transcript-level transcript abundances in TPM and counts, which are stored in the `tx_TPM` and `tx_counts` assays, respectively. <br> - `equivalence_classes.tar.gz`: A compressed directory containing equivalence classes generated by salmon for all BioSamples. Equivalence classes are typically used for differential transcript usage analyses. <br> - `parquet_dir.tar.gz`: A partitioned .parquet directory with the gene-level transcript abundances in TPM and bias-corrected counts created with the *arrow* package. <br>

搜集汇总

背景与挑战

背景概述

Soybean Expression Atlas v2 是一个于2023年发布的大豆基因表达图谱数据集，由Fabricio Almeida-Silva和THIAGO VENANCIO创建。该数据集包含基因水平和转录本水平的转录丰度数据（如TPM和计数），以及用于差异转录本使用分析的等价类文件，支持生物信息学方法开发，并以CC BY 4.0许可证开放共享。