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TheDongLab/EVscope: v1.0.1

integration_instructionsResearch softwarekeyboard_double_arrow_right Software 24 Jun 2025Publisher:Zenodo
Authors: Yiyong, Zhao; Chintalapudi, Himanshu; Xu, Ziqian; Liu, Weiqiang; Hu, Yuxuan; Grassin, Ewa; Dong, Xianjun;
Code repository: https://github.com/TheDongLab/EVscope/tree/v1.0.1

doi: 10.5281/zenodo.19171865 , 10.5281/zenodo.15577789 , 10.5281/zenodo.15577788

TheDongLab/EVscope: v1.0.1

Abstract

v1.0.1: EVscope source code + HG38 annotation reference files Code changes:- Fix Step 18: use merged SAF for meta-gene featureCounts (eliminates cross-region double-counting)- Remove ENCODE blacklist from meta-gene counting- Fix undefined variable in Step 27 HTML report- Fix hardcoded thread counts in Step 26- Remove unused imports, translate Chinese comments Annotation files (EVscope_annotations_HG38.zip, 406 MB):35 pre-built genome annotation files for HG38 (GENCODE v45):- Gene annotations: GTF, RefFlat, gene ID mapping (3,659,642 RNAs, 20 biotypes)- Meta-gene regions: merged SAF + 7 BED files (5'UTR, 3'UTR, exon, intron, promoter, downstream, intergenic)- RNA type BED: protein-coding, lncRNA, miRNA, snoRNA, snRNA, tRNA, rRNA, piRNA, pseudogenes, LINE, SINE, ERV- ENCODE blacklist v2, rRNA interval list- Total uncompressed: 5.4 GB

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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