bioRxiv/medRxiv TRiP Review Activity

363 Reviews — GigaScience — All Subjects

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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

StereoSiTE: A framework to spatially and quantitatively profile the cellular neighborhood organized iTME

Liu, X., Qu, C., Liu, C., Zhu, N., Huang, H., Teng, F., Huang, C., Luo, B., Liu, X., Xu, Y., Xie, M., Xi, F., Li, M., Wu, L., Li, Y., Chen, A., Xu, X., Liao, S., Zhang, J.

10.1101/2022.12.31.522366 — Posted: 2022-12-31 — 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

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

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

MOBFinder: a tool for MOB typing for plasmid metagenomic fragments based on language model

Feng, T., Wu, S., Zhou, H., Fang, Z.

10.1101/2023.12.06.570414 — Posted: 2023-12-07 — 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

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