miRBench datasets

Changelog

PhyloP and PhastCons conservation scores for the target gene sequence have been added to the test/train/leftout datasets as two additional columns - 'gene_phyloP' and' gene_phastCons'. 

Both of new columns contain list of conservation scores rounded to 3 decimal places, one score for each nucelotide in the gene sequence.PhyloP and PhastCons scores were obtained from:

https://hgdownload.cse.ucsc.edu/goldenPath/hg38/phyloP100way/hg38.phyloP100way.bw

https://hgdownload.cse.ucsc.edu/goldenpath/hg38/phastCons100way/hg38.phastCons100way.bw

Downloaded on 15 September 2024. 

Dataset Summary

The following listed datasets were recreated via a series of post-processing pipelines (available here) to eliminate a bias between the positive and negative classes (miRNA family imbalance) discovered in previous versions of the datasets. All have a 1:1 positive to negative class ratio. 

AGO2_eCLIP_Manakov2022_leftout.tsv.gz

AGO2_eCLIP_Manakov2022_test.tsv.gz

AGO2_eCLIP_Manakov2022_train.tsv.gz

AGO2_eCLIP_Klimentova2022_test.tsv.gz

AGO2_CLASH_Hejret2023_test.tsv.gz

AGO2_CLASH_Hejret2023_train.tsv.gz

The following listed dataset is the concatenated HybriDetector output of all the selected samples from the available Manakov sample files. It therefore contains only a raw version of the positive class of the Manakov dataset. It is the input to the series of post-process pipelines for the Manakov dataset. 

AGO2_eCLIP_Manakov2022_full_dataset.tsv.gz

The other inputs to the post-process pipelines for the Hejret and Klimentova datasets are found at the following links. 

Hejret dataset

Klimentova dataset