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- 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)
- 13:42, 4 March 2020 (diff | hist) . . (+1,518) . . N The impact of sample imbalance on identifying differentially expressed genes (Created page with "__NUMBEREDHEADINGS__ === Citation === Kun Yang, Jianzhong Li and Hong Gao, The impact of sample imbalance on identifying differentially expressed genes, 2006, BMC Bioinformati...") (current)
- 13:31, 4 March 2020 (diff | hist) . . (+102) . . Literature Studies (→Identifying differential features)
- 16:49, 28 February 2020 (diff | hist) . . (-1) . . Predicting Breast Cancer Survivability Using Data Mining Techniques (→Citation) (current)
- 16:49, 28 February 2020 (diff | hist) . . (+1,786) . . N Predicting Breast Cancer Survivability Using Data Mining Techniques (Created page with "__NUMBEREDHEADINGS__ === Citation === Sarvestani, A. S., Safavi, A. A., Parandeh, N. M., & Salehi, M., Predicting breast cancer survivability using data mining techniques, 20...")
- 16:46, 28 February 2020 (diff | hist) . . (+33) . . Literature Studies
- 16:45, 28 February 2020 (diff | hist) . . (-108) . . Literature Studies (Remove Harper, it is not based on high-througput data)
- 16:41, 28 February 2020 (diff | hist) . . (-2) . . Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data (→Outcome O1) (current)
- 16:41, 28 February 2020 (diff | hist) . . (+2,149) . . N Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data (Created page with "__NUMBEREDHEADINGS__ === Citation === Baolin Wu, Tom Abbott, David Fishman, Walter McMurray, Gil Mor, Kathryn Stone, David Ward, Kenneth Williams, Hongyu Zhao, Comparison of s...")
- 16:18, 28 February 2020 (diff | hist) . . (+30) . . Literature Studies (→Omics Workflows)
- 16:16, 28 February 2020 (diff | hist) . . (+102) . . Literature Studies (→Preprocessing high-throughput data)
- 16:11, 28 February 2020 (diff | hist) . . (+76) . . Literature Studies (→Classification)
- 16:10, 28 February 2020 (diff | hist) . . (+118) . . Literature Studies (→Identifying differential features)
- 16:07, 28 February 2020 (diff | hist) . . (-16) . . Literature Studies (→Identifying sets of features (e.g. gene set analyses))
- 16:06, 28 February 2020 (diff | hist) . . (+149) . . Literature Studies (→Identifying sets of features (e.g. gene set analyses))
- 16:05, 28 February 2020 (diff | hist) . . (+4) . . Literature Studies (→Dimension reduction)
- 16:04, 28 February 2020 (diff | hist) . . (-55) . . Literature Studies (→Identifying differential regions (e.g. DMRs))
- 16:02, 28 February 2020 (diff | hist) . . (+224) . . Literature Studies (→Identifying differential regions (e.g. DMRs))
- 15:59, 28 February 2020 (diff | hist) . . (0) . . Literature Studies (→Dimension reduction)
- 15:58, 28 February 2020 (diff | hist) . . (+1) . . Literature Studies (→Dimension reduction)
- 15:58, 28 February 2020 (diff | hist) . . (+32) . . Literature Studies (→Dimension reduction)
- 15:56, 28 February 2020 (diff | hist) . . (+54) . . Literature Studies (→Dimension reduction)
- 15:57, 25 February 2020 (diff | hist) . . (+596) . . Toward a gold standard for benchmarking gene set enrichment analysis (current)
- 15:41, 25 February 2020 (diff | hist) . . (-1) . . Toward a gold standard for benchmarking gene set enrichment analysis (→Citation)
- 15:40, 25 February 2020 (diff | hist) . . (+159) . . A general modular framework for gene set enrichment analysis (current)
- 15:38, 25 February 2020 (diff | hist) . . (+1,854) . . N Toward a gold standard for benchmarking gene set enrichment analysis (Created page with "__ NUMBEREDHEADINGS__ === Citation === Geistlinger, L., Csaba, G., Santarelli, M., Ramos, M., Schiffer, L., Law, C., ... & Zimmer, R., Toward a gold standard for benchmarking...")
- 15:31, 25 February 2020 (diff | hist) . . (+84) . . Literature Studies (→Identifying sets of features (e.g. gene set analyses))
- 15:26, 25 February 2020 (diff | hist) . . (-1) . . A general modular framework for gene set enrichment analysis (→Design for Outcome O4: Significance assessment)
- 15:26, 25 February 2020 (diff | hist) . . (-1) . . A general modular framework for gene set enrichment analysis (→Further comments and aspects)
- 15:26, 25 February 2020 (diff | hist) . . (-56) . . A general modular framework for gene set enrichment analysis (→References)
- 15:26, 25 February 2020 (diff | hist) . . (+45) . . A general modular framework for gene set enrichment analysis (→Outcome O5: Global approaches)
- 15:24, 25 February 2020 (diff | hist) . . (-70) . . A general modular framework for gene set enrichment analysis (→Study outcomes)
- 15:24, 25 February 2020 (diff | hist) . . (+21) . . A general modular framework for gene set enrichment analysis
- 15:23, 25 February 2020 (diff | hist) . . (+2,070) . . A general modular framework for gene set enrichment analysis
- 14:46, 25 February 2020 (diff | hist) . . (+82) . . A general modular framework for gene set enrichment analysis (→Outcome O2: Transformation of the gene level statistics)
- 14:45, 25 February 2020 (diff | hist) . . (+26) . . A general modular framework for gene set enrichment analysis (→Outcome O2: Transformation of the gene level statistics)
- 14:43, 25 February 2020 (diff | hist) . . (+1,718) . . A general modular framework for gene set enrichment analysis
- 14:10, 25 February 2020 (diff | hist) . . (+431) . . A general modular framework for gene set enrichment analysis
- 14:03, 25 February 2020 (diff | hist) . . (-1) . . A general modular framework for gene set enrichment analysis (→Citation)
- 14:03, 25 February 2020 (diff | hist) . . (+75) . . A general modular framework for gene set enrichment analysis (→Summary)
- 14:00, 25 February 2020 (diff | hist) . . (+1,768) . . N A general modular framework for gene set enrichment analysis (Created page with "__NUMBEREDHEADINGS__ === Citation === M Ackermann and K Strimmer, A general modular framework for gene set enrichment analysis, 2009, BMC Bioinformatics, 10:47, pages etc in a...")
- 13:54, 25 February 2020 (diff | hist) . . (+269) . . Gene set analysis methods: a systematic comparison (current)
- 13:50, 25 February 2020 (diff | hist) . . (+560) . . Gene set analysis methods: a systematic comparison
- 13:35, 25 February 2020 (diff | hist) . . (+631) . . Gene set analysis methods: a systematic comparison
- 13:20, 25 February 2020 (diff | hist) . . (+650) . . Gene set analysis methods: a systematic comparison
- 13:08, 25 February 2020 (diff | hist) . . (-81) . . Gene set analysis methods: a systematic comparison
- 13:03, 25 February 2020 (diff | hist) . . (-77) . . Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16 (→References) (current)
- 13:02, 25 February 2020 (diff | hist) . . (+19) . . Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16 (→Design for Outcome O2)
- 13:01, 25 February 2020 (diff | hist) . . (+33) . . Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16 (→Design for Outcome O1)
- 13:00, 25 February 2020 (diff | hist) . . (-138) . . Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16 (→General aspects)
- 12:59, 25 February 2020 (diff | hist) . . (-2) . . Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16 (→Outcome O2)
- 12:58, 25 February 2020 (diff | hist) . . (0) . . Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16
- 12:56, 25 February 2020 (diff | hist) . . (-70) . . Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16 (→Study outcomes)
- 12:55, 25 February 2020 (diff | hist) . . (-98) . . Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16 (→Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16)
- 12:55, 25 February 2020 (diff | hist) . . (-1) . . Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16 (→Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16)
- 12:54, 25 February 2020 (diff | hist) . . (-1) . . Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16 (→Further outcomes)
- 12:54, 25 February 2020 (diff | hist) . . (+878) . . Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16 (→Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16)
- 12:40, 25 February 2020 (diff | hist) . . (+434) . . Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16 (→Design for Outcome O2)
- 12:23, 25 February 2020 (diff | hist) . . (+29) . . Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16 (→Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16)
- 12:22, 25 February 2020 (diff | hist) . . (+1,779) . . Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16 (→Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16)
- 11:45, 25 February 2020 (diff | hist) . . (+1,665) . . N Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16 (Created page with "__NUMBEREDHEADINGS__ == Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16 == Tintle, N. L., Borchers, B., Brown, M.,...")
- 11:36, 25 February 2020 (diff | hist) . . (+115) . . Literature Studies (→Identifying sets of features (e.g. gene set analyses))
- 10:44, 25 February 2020 (diff | hist) . . (+1,441) . . Gene set analysis methods: a systematic comparison (→Gene set analysis methods: a systematic comparison)
- 10:13, 25 February 2020 (diff | hist) . . (+434) . . Gene set analysis methods: a systematic comparison (→Outcome O1)
- 10:00, 25 February 2020 (diff | hist) . . (+1,130) . . Gene set analysis methods: a systematic comparison (→Study design and evidence level)
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