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

BMC Bioinformatics

Table 2 Ribosome abundance estimation performance in three replicate synthetic datasets

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

ISSN: 1471-2105