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Table 2 Ribosome abundance estimation performance in three replicate synthetic datasets

From: DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data

Evaluation Method Dataset 1 Dataset 2 Dataset 3
Ribosome count PCC DeepShape-prime 0.9931 0.9947 0.9932
Ribomap 0.8952 0.9253 0.8680
Ribosome count MSE DeepShape-prime 87,546 70,815 157,187
Ribomap 1,216,917 854,546 2,213,367
CDS-Length-normalized ribosome abundance PCC DeepShape-prime 0.9990 0.9991 0.9981
Ribomap 0.9158 0.9381 0.9616
Ground-truth mRNA vs ribosome abundance PCC (both normalized by length) 0. 6775 0.7162 0.8252
  1. PCC: Pearson correlation coefficient between prediction and ground-truth.
  2. MSE: Mean square error between prediction and ground-truth.