Soybean Expression Atlas v2

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