bioRxiv/medRxiv TRiP Review Activity

520 Reviews — All Partners — Bioinformatics

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Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data.
Gabriel, A. A., Racle, J., Falquet, M., Jandus, C., Gfeller, D.
10.1101/2023.10.11.561826 — Posted: 2023-10-14 — Discussion: 2024-09-09  eLife
Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data
Hall, M. B., Wick, R. R., Judd, L. M., Nguyen, A. N. T., Steinig, E. J., Xie, O., Davies, M. R., Seemann, T., Stinear, T. P., Coin, L. J. M.
10.1101/2024.03.15.585313 — Posted: 2024-03-16 — Discussion: 2024-09-05  eLife
RiboSnake - a user-friendly, robust, reproducible, multipurpose and documentation-extensive pipeline for 16S rRNA gene microbiome analysis
Doerr, A.-K., Welling, J., Doerr, A., Gosch, J., Moehlen, H., Schmithausen, R., Kehrmann, J., Meyer, F., Kraiselburd, I.
10.1101/2024.08.06.606757 — Posted: 2024-08-08 — Discussion: 2024-09-04  Gigabyte
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
Identifying images in the biology literature that are problematic for people with a color-vision deficiency
Stevens, H. P., Winegar, C. V., Oakley, A. F., Piccolo, S. R.
10.1101/2023.11.29.569308 — Posted: 2023-11-30 — Discussion: 2024-08-29  eLife
ImmCellTyper: an integrated computational pipeline for systematic mining of Mass Cytometry data to assist deep immune profiling
Sun, J., Choy, D., Sompairac, N., Jamshidi, S., Mishto, M., Kordasti, S.
10.1101/2024.01.15.575790 — Posted: 2024-01-17 — Discussion: 2024-08-13  eLife
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
Detection and identification of transposable element transcripts using Long Read RNA-seq in Drosophila germline tissues
Rebollo, R., Cumunel, E., Mary, A., Sabot, F., Burlet, N., Gillet, B., Hughes, S., Siqueira Oliveira, D., Goubert, C., Fablet, M., Vieira, C., Lacroix, V.
10.1101/2023.05.27.542554 — Posted: 2023-05-30 — Discussion: 2024-08-06  Peer Community In

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