Literature DB >> 27027585

iCOBRA: open, reproducible, standardized and live method benchmarking.

Charlotte Soneson1,2, Mark D Robinson1,2.   

Abstract

Mesh：

Year:  2016        PMID： 27027585     DOI： 10.1038/nmeth.3805

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


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  6 in total

1.  BDTcomparator: a program for comparing binary classifiers.

Authors:  Kamil Fijorek; Damian Fijorek; Barbara Wisniowska; Sebastian Polak
Journal:  Bioinformatics       Date:  2011-10-13       Impact factor: 6.937

2.  ROCR: visualizing classifier performance in R.

Authors:  Tobias Sing; Oliver Sander; Niko Beerenwinkel; Thomas Lengauer
Journal:  Bioinformatics       Date:  2005-08-11       Impact factor: 6.937

3.  compcodeR--an R package for benchmarking differential expression methods for RNA-seq data.

Authors:  Charlotte Soneson
Journal:  Bioinformatics       Date:  2014-05-09       Impact factor: 6.937

4.  Detecting differential usage of exons from RNA-seq data.

Authors:  Simon Anders; Alejandro Reyes; Wolfgang Huber
Journal:  Genome Res       Date:  2012-06-21       Impact factor: 9.043

5.  Differential abundance analysis for microbial marker-gene surveys.

Authors:  Joseph N Paulson; O Colin Stine; Héctor Corrada Bravo; Mihai Pop
Journal:  Nat Methods       Date:  2013-09-29       Impact factor: 28.547

6.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.

Authors:  Mark D Robinson; Davis J McCarthy; Gordon K Smyth
Journal:  Bioinformatics       Date:  2009-11-11       Impact factor: 6.937
  6 in total
  18 in total

1.  Reproducible and replicable comparisons using SummarizedBenchmark.

Authors:  Patrick K Kimes; Alejandro Reyes
Journal:  Bioinformatics       Date:  2019-01-01       Impact factor: 6.937

2.  Bias, robustness and scalability in single-cell differential expression analysis.

Authors:  Charlotte Soneson; Mark D Robinson
Journal:  Nat Methods       Date:  2018-02-26       Impact factor: 28.547

3.  Nonparametric expression analysis using inferential replicate counts.

Authors:  Anqi Zhu; Avi Srivastava; Joseph G Ibrahim; Rob Patro; Michael I Love
Journal:  Nucleic Acids Res       Date:  2019-10-10       Impact factor: 16.971

4.  Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification.

Authors:  Michael I Love; Charlotte Soneson; Rob Patro
Journal:  F1000Res       Date:  2018-06-27

Review 5.  Essential guidelines for computational method benchmarking.

Authors:  Lukas M Weber; Wouter Saelens; Robrecht Cannoodt; Charlotte Soneson; Alexander Hapfelmeier; Paul P Gardner; Anne-Laure Boulesteix; Yvan Saeys; Mark D Robinson
Journal:  Genome Biol       Date:  2019-06-20       Impact factor: 13.583

6.  Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences.

Authors:  Anqi Zhu; Joseph G Ibrahim; Michael I Love
Journal:  Bioinformatics       Date:  2019-06-01       Impact factor: 6.937

7.  Temporal dynamics in meta longitudinal RNA-Seq data.

Authors:  Sunghee Oh; Congjun Li; Ransom L Baldwin; Seongho Song; Fang Liu; Robert W Li
Journal:  Sci Rep       Date:  2019-01-24       Impact factor: 4.379

8.  diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering.

Authors:  Lukas M Weber; Malgorzata Nowicka; Charlotte Soneson; Mark D Robinson
Journal:  Commun Biol       Date:  2019-05-14

9.  Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications.

Authors:  Koen Van den Berge; Fanny Perraudeau; Charlotte Soneson; Michael I Love; Davide Risso; Jean-Philippe Vert; Mark D Robinson; Sandrine Dudoit; Lieven Clement
Journal:  Genome Biol       Date:  2018-02-26       Impact factor: 13.583

10.  Comparative analysis of differential gene expression tools for RNA sequencing time course data.

Authors:  Daniel Spies; Peter F Renz; Tobias A Beyer; Constance Ciaudo
Journal:  Brief Bioinform       Date:  2019-01-18       Impact factor: 11.622
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