BioBench Atlas
Atlas/Papers/Work detail

paper · benchmark creator

Comprehensive benchmark of differential transcript usage analysis for bulk and single-cell RNA sequencing

Data Science in Systems Biology, Technical University of Munich · Chair of Computational Systems Biology, University of Hamburg · Institute for Advanced Study, Technical University of Munich · National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health · Institute of Mathematics and Computer Science, University of Southern Denmark · Munich Data Science Institute (MDSI), Technical University of Munich · Department of Computer Science, Bioinformatics, Vrije Universiteit Amsterdam · 2025-09-11

Relationship layer

Benchmark usage

This table records what the work did with each benchmark before attempting to normalize a run. Partial claims remain visible without being treated as comparable evaluations.

benchmark creation

comprehensive-benchmark-of-differential-transcript-usa-comprehensive-benchmark-of-differential-transcript-usage-analysis-for-bu-1-use

Non-evaluationunknown

Benchmark: Comprehensive benchmark of differential transcript usage analysis for bulk and single-cell RNA sequencing · version Not reported

Selection
not applicable
Models
Not reported / not applicable
Metrics
Not reported / not applicable
Linked runs
None

Not reported / unresolved: No single finite primary item inventory is reported for the reusable benchmark matrix.; No benchmark version or separate release date is stated.; The paper does not explicitly assign a Registry access level.

AI-assisted double-pass extraction; values are limited to independently supported claims.

Evidence
  • section: Abstract
    Supports: /relation_type
  • page: Article title
    Supports: /benchmark_id

evaluation

comprehensive-benchmark-of-differential-transcript-usa-comprehensive-benchmark-of-differential-transcript-usage-analysis-for-bu-2-use

Partialunknown

Benchmark: Comprehensive benchmark of differential transcript usage analysis for bulk and single-cell RNA sequencing · version Not reported

Selection
not reported
Models
Not reported / not applicable
Metrics
Not reported / not applicable
Linked runs
None

Not reported / unresolved: The parameter matrix does not provide one uniform realized evaluation n.; Random seeds and versions of most evaluated DTU methods are not reported.; Unlabeled graphical scores were not estimated.; benchmark version; realized n/scope; metric; numeric result; prompt and tools; grader and repeats; exact model

Owner-reviewed conservative publication: the creator evaluation is retained only as a partial relationship; conflicted settings and outcomes are omitted pending manual reconciliation.

Evidence
  • section: Overall performance of DTU detection
    Supports: /relation_type
  • page: Article title
    Supports: /benchmark_id

evaluation

comprehensive-benchmark-of-differential-transcript-usa-comprehensive-benchmark-of-differential-transcript-usage-analysis-for-bu-3-use

Partialunknown

Benchmark: Comprehensive benchmark of differential transcript usage analysis for bulk and single-cell RNA sequencing · version Not reported

Selection
not reported
Models
Not reported / not applicable
Metrics
Not reported / not applicable
Linked runs
None

Not reported / unresolved: Simulation repeat count and random seed are not reported.; The varying balanced and unbalanced dataset sizes prevent one uniform realized n.; benchmark version; realized n/scope; metric; numeric result; prompt and tools; grader and repeats; exact model

Owner-reviewed conservative publication: the creator evaluation is retained only as a partial relationship; conflicted settings and outcomes are omitted pending manual reconciliation.

Evidence
  • section: Performance in single-cell data
    Supports: /relation_type
  • page: Article title
    Supports: /benchmark_id

evaluation

comprehensive-benchmark-of-differential-transcript-usa-comprehensive-benchmark-of-differential-transcript-usage-analysis-for-bu-4-use

Partialunknown

Benchmark: Comprehensive benchmark of differential transcript usage analysis for bulk and single-cell RNA sequencing · version Not reported

Selection
not reported
Models
Not reported / not applicable
Metrics
Not reported / not applicable
Linked runs
None

Not reported / unresolved: Simulation repeat count and random seed are not reported.; The unbalanced meta-cell evaluation has no single reported realized cell count.; benchmark version; realized n/scope; metric; numeric result; prompt and tools; grader and repeats; exact model

Owner-reviewed conservative publication: the creator evaluation is retained only as a partial relationship; conflicted settings and outcomes are omitted pending manual reconciliation.

Evidence
  • section: Performance in single-cell data
    Supports: /relation_type
  • page: Article title
    Supports: /benchmark_id

evaluation

comprehensive-benchmark-of-differential-transcript-usa-comprehensive-benchmark-of-differential-transcript-usage-analysis-for-bu-5-use

Partialunknown

Benchmark: Comprehensive benchmark of differential transcript usage analysis for bulk and single-cell RNA sequencing · version Not reported

Selection
not reported
Models
Not reported / not applicable
Metrics
Not reported / not applicable
Linked runs
None

Not reported / unresolved: The realized sample count after removing 10 matching samples is not explicitly reported.; The real dataset has no simulated ground truth.; F1 dots without printed numeric labels were not estimated.; benchmark version; realized n/scope; metric; numeric result; prompt and tools; grader and repeats; exact model

Owner-reviewed conservative publication: the creator evaluation is retained only as a partial relationship; conflicted settings and outcomes are omitted pending manual reconciliation.

Evidence
  • section: Benchmarking with a real transcriptome dataset
    Supports: /relation_type
  • page: Article title
    Supports: /benchmark_id

evaluation

comprehensive-benchmark-of-differential-transcript-usa-comprehensive-benchmark-of-differential-transcript-usage-analysis-for-bu-6-use

Partialunknown

Benchmark: Comprehensive benchmark of differential transcript usage analysis for bulk and single-cell RNA sequencing · version Not reported

Selection
not reported
Models
Not reported / not applicable
Metrics
Not reported / not applicable
Linked runs
None

Not reported / unresolved: The body and Figure 7 caption disagree about the evaluated method list.; No ground-truth performance metric is reported for the real time-series dataset.; Conflicted scope-n claim omitted after independent verification; the evaluation relationship is published conservatively.; Conflicted result claim omitted after independent verification; the evaluation relationship is published conservatively.; benchmark version; realized n/scope; metric; numeric result; prompt and tools; grader and repeats; exact model

Owner-reviewed conservative publication: the creator evaluation is retained only as a partial relationship; conflicted settings and outcomes are omitted pending manual reconciliation.

Evidence
  • section: Time series IS analysis
    Supports: /relation_type
  • page: Article title
    Supports: /benchmark_id

Normalized evaluation runs

This source has no normalized model run. It may be a creator-only source or a partial/non-evaluation benchmark use.