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
- 16:49, 1 May 2021 (diff | hist) . . (+81) . . Literature Studies (→Results from Literature)
- 14:48, 2 February 2021 (diff | hist) . . (+1,488) . . N Benchmarking Quantitative Performance in Label-Free Proteomics (Created page with "__NUMBEREDHEADINGS__ === Citation === Dowell JA, Wright LJ, Armstrong EA, Denu JM (2021). Benchmarking Quantitative Performance in Label-Free Proteomics. ACS Omega. [https://d...") (current)
- 14:44, 2 February 2021 (diff | hist) . . (+93) . . Literature Studies (→Omics Workflows)
- 14:41, 2 February 2021 (diff | hist) . . (0) . . Literature Studies (→Results from Literature)
- 14:40, 2 February 2021 (diff | hist) . . (-2) . . Literature Studies (→Results from Literature)
- 14:39, 2 February 2021 (diff | hist) . . (+2) . . Literature Studies (→Results from Literature)
- 14:38, 2 February 2021 (diff | hist) . . (+2) . . Literature Studies (→Results from Literature)
- 14:36, 2 February 2021 (diff | hist) . . (+1) . . Literature Studies (→Results from Literature)
- 14:34, 2 February 2021 (diff | hist) . . (-1) . . NormalyzerDE: Online Tool for Improved Normalization of Omics Expression Data and High-Sensitivity Differential Expression Analysis (→Citation) (current)
- 14:33, 2 February 2021 (diff | hist) . . (-2) . . The effects of nonignorable missing data on label-free mass spectrometry proteomics experiments (→Citation) (current)
- 14:32, 2 February 2021 (diff | hist) . . (-2) . . A comparative study of evaluating missing value imputation methods in label-free proteomics (→Citation) (current)
- 14:31, 2 February 2021 (diff | hist) . . (-16) . . A comparative study of evaluating missing value imputation methods in label-free proteomics
- 14:25, 2 February 2021 (diff | hist) . . (+531) . . N A comparative study of evaluating missing value imputation methods in label-free proteomics (Created page with "=== Citation === O'Brien JJ, Gunawardena HP, Paulo JA, Chen X, Ibrahim JG, Gygi SP, Qaqish BF (2018). The effects of nonignorable missing data on label-free mass spectrometry...")
- 14:23, 2 February 2021 (diff | hist) . . (+118) . . Literature Studies (→Imputation methods for missing values)
- 17:23, 8 November 2020 (diff | hist) . . (+1,645) . . N Simultaneous Improvement in the Precision, Accuracy and Robustness of Label-free Proteome Quantification by Optimizing Data Manipulation Chains (Created page with "__NUMBEREDHEADINGS__ === Citation === Tang J, Fu J, Wang Y, Luo Y, Yang Q, Li B, Tu G, Hong J, Cui X, Chen Y, Yao L. Simultaneous improvement in the precision, accuracy, and r...") (current)
- 17:21, 8 November 2020 (diff | hist) . . (+170) . . Literature Studies (→Omics Workflows)
- 12:56, 9 March 2020 (diff | hist) . . (+104) . . Literature Studies (→Identifying differential features)
- 12:20, 9 March 2020 (diff | hist) . . (+180) . . Literature Studies (→Identifying differential features)
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