Soybean Expression Atlas v2

Overview This directory contains important files created during the construction of the Soybean Expression Atlas v2. Directory structure Here, you can find the following files: - `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. - `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. - `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. - `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.