bioRxiv/medRxiv TRiP Review Activity

264 Reviews — GigaScience — Bioinformatics

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CAT Bridge: an efficient toolkit for compound-transcript association mining from multi-omics data
Yang, B., Meng, T., Wang, X., Li, J., Zhao, S., Wang, Y., Yi, S., Zhou, Y., Zhang, Y., Li, L., Guo, L.
10.1101/2024.01.21.576587 — Posted: 2024-01-24 — Discussion: 2024-12-05  GigaScience
demuxSNP: supervised demultiplexing scRNAseq using cell hashing and SNPs
Lynch, M. P., Wang, Y., Gatto, L., Culhane, A. C.
10.1101/2024.04.22.590526 — Posted: 2024-04-26 — Discussion: 2024-12-05  GigaScience
An Unsupervised Contrastive Learning Model for Data Integration of Spatially Resolved Transcriptomics
Zhang, C., Liu, L., Zhang, Y., Li, M., Fang, S., Kang, Q., Chen, A., Xu, X., Zhang, Y., Li, Y.
10.1101/2023.08.08.552402 — Posted: 2023-08-12 — Discussion: 2024-11-23  GigaScience
Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD)
Frazer, S. A., Baghbanzadeh, M., Rahnavard, A., Crandall, K. A., Oakley, T. H.
10.1101/2024.02.12.579993 — Posted: 2024-02-14 — Discussion: 2024-11-23  GigaScience
CoCoPyE: feature engineering for learning and prediction of genome quality indices
Birth, N., Leppich, N., Schirmacher, J., Andreae, N., Steinkamp, R., Blanke, M., Meinicke, P.
10.1101/2024.02.07.579156 — Posted: 2024-02-10 — Discussion: 2024-11-23  GigaScience
A data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence (MISIP)
Simpson, A. M. R., Wood Charlson, E. M., Smith, M., Beilsmith, K., Koch, B., Walls, R. L., Wilhelm, R. C.
10.1101/2023.07.13.548835 — Posted: 2023-07-17 — Discussion: 2024-11-23  GigaScience
V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation
Fuhrmann, L., Jablonski, K. P., Topolsky, I., Batavia, A. A., Borgsmueller, N., Icer Baykal, P., Carrara, M., Chen, C., Dondi, A., Dragan, M., Dreifuss, D., John, A., Langer, B., Okoniewski, M., du Plessis, L., Schmitt, U., Singer, F., Stadler, T., Beerenwinkel, N.
10.1101/2023.10.16.562462 — Posted: 2023-10-16 — Discussion: 2024-11-10  GigaScience
TooManyCellsInteractive: a visualization tool for dynamic exploration of single-cell data
Klamann, C., Lau, C., Schwartz, G. W.
10.1101/2023.06.16.544954 — Posted: 2023-06-18 — Discussion: 2024-09-03  GigaScience
Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data
Assmann, E., Agrawal, S., Orschler, L., Böttcher, S., Lackner, S., Hölzer, M.
10.1101/2023.06.02.543047 — Posted: 2023-06-02 — Discussion: 2024-08-12  GigaScience
Deciphering Cancer Genomes with GenomeSpy: A Grammar-Based Visualization Toolkit
Lavikka, K., Oikkonen, J., Li, Y., Muranen, T., Micoli, G., Marchi, G., Lahtinen, A., Huhtinen, K., Lehtonen, R., Hietanen, S., Hynninen, J., Virtanen, A., Hautaniemi, S.
10.1101/2023.10.06.561159 — Posted: 2023-10-06 — Discussion: 2024-08-12  GigaScience

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