User contributions
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- 11:06, 3 April 2024 (diff | hist) . . (+1,599) . . N A Comprehensive Survey of Statistical Approaches for Differential Expression Analysis in Single-Cell RNA Sequencing Studies (Created page with "__NUMBEREDHEADINGS__ === Citation === Das, Samarendra, Anil Rai, Michael L. Merchant, Matthew C. Cave, and Shesh N. Rai. "A comprehensive survey of statistical approaches for...") (current)
- 11:04, 3 April 2024 (diff | hist) . . (+148) . . Literature Studies (→Identifying differential features) (current)
- 07:31, 16 January 2024 (diff | hist) . . (+128) . . Literature Studies (New study about metagenomic classifier)
- 07:27, 16 January 2024 (diff | hist) . . (+149) . . Benchmarking Studies in Computational Biology (Neues Paper: Challenges and best practices in omics benchmarking) (current)
- 07:58, 27 October 2023 (diff | hist) . . (+184) . . Literature Studies (AI section added)
- 07:55, 27 October 2023 (diff | hist) . . (+2) . . Literature Studies (→Single Cell Omics)
- 07:55, 27 October 2023 (diff | hist) . . (-2) . . Literature Studies (→Single Cell Omics)
- 07:54, 27 October 2023 (diff | hist) . . (+42) . . Literature Studies (Table Title added)
- 07:54, 27 October 2023 (diff | hist) . . (+214) . . Literature Studies (Single Cell Omics added)
- 07:29, 25 October 2023 (diff | hist) . . (+779) . . N Test title (Created page with "__NUMBEREDHEADINGS__ === Citation === Authors, title, year, journal, volume, pages etc in any possible citation style. [https://doi.org/10.1371/journal.pone.0074335] === Su...") (current)
- 07:27, 25 October 2023 (diff | hist) . . (+36) . . Literature Studies (TEst)
- 16:31, 24 October 2023 (diff | hist) . . (-1) . . Catalyst: Fast and flexible modeling of reaction networks (current)
- 16:31, 24 October 2023 (diff | hist) . . (+824) . . N Catalyst: Fast and flexible modeling of reaction networks (Creating a short page without deep reading)
- 16:25, 24 October 2023 (diff | hist) . . (+84) . . Literature Studies (Catalyst added)
- 16:01, 18 February 2022 (diff | hist) . . (+1,557) . . N Analysing microbiome intervention design studies: Comparison of alternative multivariate statistical methods (Created page with "__NUMBEREDHEADINGS__ === Citation === Khomich, M., Måge, I., Rud, I., & Berget, I. (2021). Analysing microbiome intervention design studies: Comparison of alternative multiva...") (current)
- 16:00, 18 February 2022 (diff | hist) . . (+1,567) . . N Benchmarking of 16S rRNA gene databases using known strain sequences (Created page with "__NUMBEREDHEADINGS__ === Citation === Dixit, K., Davray, D., Chaudhari, D., Kadam, P., Kshirsagar, R., Shouche, Y., ... & Saroj, S. D. (2021). Benchmarking of 16S rRNA gene da...") (current)
- 15:59, 18 February 2022 (diff | hist) . . (+1,627) . . N Evaluation of the microba community profiler for taxonomic profiling of metagenomic datasets from the human gut microbiome (Created page with "__NUMBEREDHEADINGS__ === Citation === Parks, D. H., Rigato, F., Vera-Wolf, P., Krause, L., Hugenholtz, P., Tyson, G. W., & Wood, D. L. (2021). Evaluation of the microba commun...") (current)
- 15:57, 18 February 2022 (diff | hist) . . (+1,582) . . N Distribution-based comprehensive evaluation of methods for differential expression analysis in metatranscriptomics (Created page with "__NUMBEREDHEADINGS__ === Citation === Cho, H., Liu, C., Tang, B., Lin, B. M., Roach, J., de Aguiar Ribeiro, A., ... & Wu, D. (2021). Distribution-based comprehensive evaluatio...") (current)
- 15:56, 18 February 2022 (diff | hist) . . (+1,576) . . N A benchmark of genetic variant calling pipelines using metagenomic short-read sequencing (Created page with "__NUMBEREDHEADINGS__ === Citation === Andreu-Sánchez, S., Chen, L., Wang, D., Augustijn, H. E., Zhernakova, A., & Fu, J. (2021). A benchmark of genetic variant calling pipeli...") (current)
- 15:55, 18 February 2022 (diff | hist) . . (+1,527) . . N LEMMI: a continuous benchmarking platform for metagenomics classifiers (Created page with "__NUMBEREDHEADINGS__ === Citation === Seppey, M., Manni, M., & Zdobnov, E. M. (2020). LEMMI: a continuous benchmarking platform for metagenomics classifiers. Genome research,...") (current)
- 15:53, 18 February 2022 (diff | hist) . . (+1,575) . . N Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data (Created page with "__NUMBEREDHEADINGS__ === Citation === Calgaro, M., Romualdi, C., Waldron, L., Risso, D., & Vitulo, N. (2020). Assessment of statistical methods from single cell, bulk RNA-seq,...") (current)
- 15:51, 18 February 2022 (diff | hist) . . (+1,548) . . N Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches (Created page with "__NUMBEREDHEADINGS__ === Citation === Nearing, J. T., Douglas, G. M., Comeau, A. M., & Langille, M. G. (2018). Denoising the Denoisers: an independent evaluation of microbiome...") (current)
- 15:50, 18 February 2022 (diff | hist) . . (+1,584) . . N Mockrobiota: a public resource for microbiome bioinformatics benchmarking (Created page with "__NUMBEREDHEADINGS__ === Citation === Bokulich, N. A., Rideout, J. R., Mercurio, W. G., Shiffer, A., Wolfe, B., Maurice, C. F., ... & Caporaso, J. G. (2016). mockrobiota: a pu...") (current)
- 15:47, 18 February 2022 (diff | hist) . . (+1,148) . . Literature Studies (→Microbiome)
- 15:16, 18 February 2022 (diff | hist) . . (+1,667) . . N Benchmark of data processing methods and machine learning models for gut microbiome-based diagnosis of inflammatory bowel disease (Created page with "__NUMBEREDHEADINGS__ === Citation === Kubinski R, Djamen-Kepaou J-Y, Zhanabaev T, Hernandez-Garcia A, Bauer S, Hildebrand F, Korcsmaros T, Karam S, Jantchou P, Kafi K and Mart...") (current)
- 15:15, 18 February 2022 (diff | hist) . . (+1,496) . . N Comparative study of classifiers for human microbiome data (Created page with "__NUMBEREDHEADINGS__ === Citation === Wang, X. W., & Liu, Y. Y. (2020). Comparative study of classifiers for human microbiome data. Medicine in microecology, 4, 100013. [http...") (current)
- 15:14, 18 February 2022 (diff | hist) . . (+1,585) . . N Comprehensive benchmarking and ensemble approaches for metagenomic classifiers (Created page with "__NUMBEREDHEADINGS__ === Citation === McIntyre, A. B., Ounit, R., Afshinnekoo, E., Prill, R. J., Hénaff, E., Alexander, N., ... & Mason, C. E. (2017). Comprehensive benchmark...") (current)
- 15:13, 18 February 2022 (diff | hist) . . (+362) . . Literature Studies (→Microbiome)
- 14:51, 18 February 2022 (diff | hist) . . (+1,514) . . N Benchmarking Metagenomics Tools for Taxonomic Classification (Created page with "__NUMBEREDHEADINGS__ === Citation === Simon, H. Y., Siddle, K. J., Park, D. J., & Sabeti, P. C. (2019). Benchmarking metagenomics tools for taxonomic classification. Cell, 178...") (current)
- 14:50, 18 February 2022 (diff | hist) . . (+87) . . Literature Studies (→Microbiome)
- 14:47, 18 February 2022 (diff | hist) . . (+1,602) . . N A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling (Created page with "__NUMBEREDHEADINGS__ === Citation === D’Amore, R., Ijaz, U. Z., Schirmer, M., Kenny, J. G., Gregory, R., Darby, A. C., ... & Hall, N. (2016). A comprehensive benchmarking st...") (current)
- 14:46, 18 February 2022 (diff | hist) . . (+139) . . Literature Studies (→Microbiome)
- 14:44, 18 February 2022 (diff | hist) . . (+1,587) . . N Evaluating supervised and unsupervised background noise correction in human gut microbiome data (Created page with "__NUMBEREDHEADINGS__ === Citation === Briscoe, L., Balliu, B., Sankararaman, S., Halperin, E., & Garud, N. R. (2022). Evaluating supervised and unsupervised background noise c...") (current)
- 14:43, 18 February 2022 (diff | hist) . . (+127) . . Literature Studies (→Microbiome)
- 14:38, 18 February 2022 (diff | hist) . . (+1,625) . . N Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases (Created page with "__NUMBEREDHEADINGS__ === Citation === Lloréns-Rico, V., Vieira-Silva, S., Gonçalves, P. J., Falony, G., & Raes, J. (2021). Benchmarking microbiome transformations favors exp...") (current)
- 14:37, 18 February 2022 (diff | hist) . . (+176) . . Literature Studies (→Microbiome)
- 14:33, 18 February 2022 (diff | hist) . . (+1,605) . . N Microbiome differential abundance methods produce different results across 38 datasets (Created page with "__NUMBEREDHEADINGS__ === Citation === Nearing, J. T., Douglas, G. M., Hayes, M. G., MacDonald, J., Desai, D. K., Allward, N., ... & Langille, M. G. (2022). Microbiome differen...") (current)
- 14:30, 18 February 2022 (diff | hist) . . (0) . . Literature Studies (→Microbiome)
- 14:29, 18 February 2022 (diff | hist) . . (+206) . . Literature Studies (→Results from Literature)
- 11:23, 27 August 2021 (diff | hist) . . (+490) . . Literature Studies (4 additional imputation benchmark studies (for scRNAseq))
- 09:34, 22 June 2021 (diff | hist) . . (+60) . . Literature Studies
- 08:08, 22 June 2021 (diff | hist) . . (+289) . . Literature Studies
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