bioRxiv/medRxiv TRiP Review Activity

253 Reviews — GigaScience — Bioinformatics

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scfetch: an R package to access and format single-cell RNA sequencing datasets from public repositories
Song, Y., Gao, J., Wang, J.
10.1101/2023.11.18.567507 — Posted: 2023-11-20 — Discussion: 2026-04-28  GigaScience
HVRLocator: A Computationally Efficient Tool for Identifying Hypervariable Regions in 16S rRNA Big Datasets
Arboleda-Baena, C., Borim Correa, F., Saraiva, J. P., Castillo, S., Kasmanas, J. C., Chatzinotas, A., Jurburg, S. D.
10.1101/2025.07.24.666487 — Posted: 2025-07-29 — Discussion: 2026-04-28  GigaScience
MADRe: Strain-Level Metagenomic Classification Through Assembly-Driven Database Reduction
Lipovac, J., Sikic, M., Vicedomini, R., Krizanovic, K.
10.1101/2025.05.12.653324 — Posted: 2025-05-15 — Discussion: 2026-04-10  GigaScience
scDenorm: a denormalisation tool for integrating single-cell transcriptomics data
Huang, Y., Pournara, A. V., Ao, Y., Yang, L., Zhang, H., Zhang, Y., Liu, S., Brazma, A., Papatheodorou, I., Yang, X., Shi, M., Miao, Z.
10.1101/2025.05.10.653289 — Posted: 2025-05-15 — Discussion: 2026-04-09  GigaScience
Comparative analysis of eccDNA and circRNA tools shows increased accuracy of tool combination
Zabala, A., Ascension, A. M., Prada-Luengo, I., Otaegui, D.
10.1101/2025.07.14.664708 — Posted: 2025-07-18 — Discussion: 2026-03-20  GigaScience
Enhanced semantic classification of microbiome sample origins using Large Language Models (LLMs)
Gaio, D., Tackmann, J., Perez-Molphe-Montoya, E., Napflin, N., Patsch, D., Malfertheiner, L., von Mering, C.
10.1101/2025.04.24.650461 — Posted: 2025-04-27 — Discussion: 2026-02-24  GigaScience
Graph-Regularized Optimal Transport for Single-Cell Data Integration
Wang, Z., Zhan, Q., Shen, L.
10.1101/2024.10.30.621072 — Posted: 2024-11-02 — Discussion: 2026-02-24  GigaScience
nf-core/proteinfamilies: A scalable pipeline for the generation of protein families
Karatzas, E., Beracochea, M., Baltoumas, F. A., Aplakidou, E., Richardson, L., Fellows Yates, J. A., Lundin, D., nf-core community, , Buluc, A., Kyrpides, N., Georgakopoulos-Soares, I., Pavlopoulos, G. A., Finn, R. D.
10.1101/2025.08.12.670010 — Posted: 2025-08-16 — Discussion: 2026-01-29  GigaScience
SpaceBF: Spatial coexpression analysis using Bayesian Fused approaches in spatial omics datasets
Seal, S., Neelon, B.
10.1101/2025.03.29.646124 — Posted: 2025-04-03 — Discussion: 2026-01-29  GigaScience
Federated Knowledge Retrieval Elevates Large Language Model Performance on Biomedical Benchmarks
Joy, J., Su, A. I.
10.1101/2025.08.01.668022 — Posted: 2025-08-02 — Discussion: 2026-01-29  GigaScience

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