bioRxiv/medRxiv TRiP Review Activity

248 Reviews — GigaScience — Bioinformatics

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GTestimate: Improving relative gene expression estimation in scRNA-seq using the Good-Turing estimator
Fahrenberger, M., Esk, C., von Haeseler, A.
10.1101/2024.07.02.601501 — Posted: 2024-07-03 — Discussion: 2025-10-30  GigaScience
GFFx: A Rust-based suite of utilities for ultra-fast genomic feature extraction
Chen, B., Dongya, W., Zhang, G.
10.1101/2025.08.08.669426 — Posted: 2025-08-12 — Discussion: 2025-10-30  GigaScience
EssSubgraph improves performance and generalizability of mammalian essential gene prediction with large networks
wen, h., Carpenter, S., McGinnis, K., Nelson, A., Smith, K., hong, t.
10.1101/2025.07.21.665218 — Posted: 2025-07-25 — Discussion: 2025-10-30  GigaScience
Reproducible processing of TCGA regulatory networks
Fanfani, V., Shutta, K. H., Mandros, P., Fischer, J., Saha, E., Micheletti, S., Chen, C., Ben Guebila, M., Lopes-Ramos, C. M., Quackenbush, J.
10.1101/2024.11.05.622163 — Posted: 2024-11-07 — Discussion: 2025-10-30  GigaScience
WaveSeekerNet: Accurate Prediction of Influenza A Virus Subtypes and Host Source Using Attention-Based Deep Learning
Nguyen, H.-H., Rudar, J., Lesperance, N., Vernygora, O., Taylor, G. W., Laing, C., Lapen, D., Leung, C. K., Lung, O.
10.1101/2025.02.25.639900 — Posted: 2025-02-28 — Discussion: 2025-09-30  GigaScience
Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing.
Chang, J. J.-Y., Yang, X., Teng, H., Reames, B., Corbin, V., Coin, L. J. M.
10.1101/2024.10.25.620206 — Posted: 2024-10-25 — Discussion: 2025-09-30  GigaScience
SPEX: A modular end-to-end analytics tool for spatially resolved omics of tissues
Pechuan Jorge, X., Li, X., Risom, T., Zubkov, A., Tabatsky, E., Prilipko, A., Ye, X., Shi, Z., Nowicka, m., Peale, F., Hibar, D., Ziai, J., Jesudason, R., Orlova, D.
10.1101/2022.08.22.504841 — Posted: 2022-08-23 — Discussion: 2025-09-30  GigaScience
Nanopore- and AI-empowered metagenomic viability inference
Urel, H., Benassou, S., Reska, T., Marti, H., Rayo, E., Martin, E. J., Schloter, M., Ferguson, J. M., Kesselheim, S., Borel, N., Urban, L.
10.1101/2024.06.10.598221 — Posted: 2024-06-11 — Discussion: 2025-09-30  GigaScience
SeuratExtend: Streamlining Single-Cell RNA-Seq Analysis Through an Integrated and Intuitive Framework
Hua, Y., Weng, L., Zhao, F., Rambow, F.
10.1101/2024.08.01.606144 — Posted: 2024-08-04 — Discussion: 2025-08-04  GigaScience
Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database
Ikeda, S., Zou, Z., Bono, H., Moriya, Y., Kawashima, S., Katayama, T., Oki, S., Ohta, T.
10.1101/2025.02.17.638570 — Posted: 2025-02-22 — Discussion: 2025-07-08  GigaScience

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