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.