Difference between revisions of "Literature Studies"
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| 2013 || García-Torres M || [[Comparison of metaheuristic strategies for peakbin selection in proteomic mass spectrometry data]] | | 2013 || García-Torres M || [[Comparison of metaheuristic strategies for peakbin selection in proteomic mass spectrometry data]] | ||
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+ | | 2013 || Horvatovich P || [[Data Preprocessing for Biomarker Discovery]] | ||
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| 2014 || || [[Normalyzer: A Tool for Rapid Evaluation of Normalization Methods for Omics Data Sets]] | | 2014 || || [[Normalyzer: A Tool for Rapid Evaluation of Normalization Methods for Omics Data Sets]] |
Revision as of 15:45, 27 February 2020
Page summary |
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Here outcomes of benchmarking studies from the literature are collected. The primary aim is a comprehensive overview about neutral benchmark studies, i.e. assessments which were performed independenty on publication of a new approach. Studies which are not neutral are put in brackets. The focus is on computational methods for analyzing experimental data (instead of comparing experimental techniques or platforms). Please extend this list by creating a new page and adding a link below. |
Contents
1 Results from Literature
1.1 Classification
2003
2005
2016
1.2 Selection of Differential Features and Regions
1.2.1 Identifying differential features
2006
2010
2017
- Identification of differentially expressed peptides in high-throughput proteomics data
- In-depth method assessments of differentially expressed protein detection for shotgun proteomics data with missing values
- Strategies for analyzing bisulfite sequencing data
2018
1.2.2 Identifying differential regions (e.g. DMRs)
2015
- De novo identification of differentially methylated regions in the human genome
- MethylAction: detecting differentially methylated regions that distinguish biological subtypes
- metilene: Fast and sensitive calling of differentially methylated regions from bisulfite sequencing data
2016
- seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data
- Statistical methods for detecting differentially methylated regions based on MethylCap-seq data
2017
2018
- Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus
- DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts
- MethCP: Differentially Methylated Region Detection with Change Point Models (bioRxiv)
1.2.3 Identifying sets of features (e.g. gene set analyses)
2009
- A general modular framework for gene set enrichment analysis
- Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16
2018
2020
1.2.4 Dimension reduction
2008
2015