A record of changes, improvements, and new features across CLASHub releases.
Analyzer V2 And Public Data
- New CLASH V2, miRNA-seq V2, and RNA-seq V2 can retrieve supported public sequencing data directly from run or study accessions.
- Improve Public-data requests check archive metadata, sample identity, species, read layout, file size, and checksums before analysis.
- Improve Study accessions open a sample-selection step, while explicitly entered SRR runs remain separate samples.
Adapter And UMI Processing
- New Added a shared V2 read-structure workflow across CLASH, miRNA-seq, and RNA-seq.
- Improve AI-assisted protocol review can propose adapter and UMI candidates from public method information; deterministic read evidence and remapping safety checks decide what is executed.
- Privacy FASTQ sequences and read names are not sent to the AI protocol reviewer.
V2 Results
- Improve miRNA-seq V2 reports raw counts, CPM, isomiR information, preprocessing records, and a multi-sample HTML report.
- Improve RNA-seq V2 produces Counts and TPM matrices for independent samples, with optional exon and intron count matrices.
- Evidence Analyzer results remain private job files and are not automatically imported into the public CLASHub Database.
CLASH V2 Analyzer
- New Replaced the public legacy CLASH Analyzer entry with CLASH V2 for Human, Mouse, Drosophila, and C. elegans.
- New Added AGO peak-supported candidate binding-site prediction alongside read-supported Direct chimera analysis.
- Improve Integrated results distinguish
direct, ago_peak, and direct+ago_peak evidence.
Analysis And Reporting
- Improve Added species-specific V9 static-site catalogs, pairing displays, genomic target regions, conservation annotations, and exact-site Direct/AGO merging.
- Improve Results now include an HTML analysis report, a filtered miRNA-target CSV, and an AGO coverage track.
- Evidence AGO peak rows are predicted candidate sites supported by AGO-enriched target-read coverage; they are not labeled as direct chimera evidence.
CLASHub AI Beta
- New Implemented an AI-assisted analysis layer for internal validation, designed to help users query CLASHub resources and summarize curated evidence.
- Improve The AI-assisted workflow is not yet publicly available while validation and institutional review are in progress.
CLASHub AI Beta
- New Added CLASHub AI Beta, allowing users to access CLASHub database-related functions through a natural language interface.
Initial Release
- Data Launched with CLASH data from 25 distinct cell lines or tissues across four model organisms: Human, Mouse, Drosophila, and C. elegans, comprising 146 datasets.
- Data Includes 55 published and 91 newly generated CLASH datasets, with 15 cell lines or tissues not previously reported in the literature.
- Data Includes 50 ZSWIM8 knockout datasets providing insights into target-directed microRNA degradation (TDMD).
- Data Gene expression profiling: 245 RNA-seq datasets from 44 cell lines or tissues.
- Data miRNA expression profiling: 157 miRNA-seq datasets across 25 cell types.
- New Database search interface for CLASH targets, gene expression, and miRNA expression with step-by-step species and cell line selection.
- New Analyzer tool supporting CLASH data processing, miRNA-seq analysis, RNA-seq analysis, and cumulative fraction curve generation.
- New Experimental validation of ATP6V1G1 as a novel TDMD trigger for miR-335, and canonical targets for miR-18a-5p.
