Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: bioconductor: ROTS

https://packages.ecosyste.ms/registries/bioconductor.org/packages/ROTS

Reproducibility-Optimized Test Statistic
1 version
Latest release: about 1 year ago
2 dependent packages
20,010 downloads total

Papers Mentioning ROTS 20

Benchmarking RNA-seq differential expression analysis methods using spike-in and simulation data
Cited by: 20
Author(s): Bukyung Baik, Susan A. Yoon, Dougu Nam
Software Mentions: 8
Published: over 4 years ago

10.1128/mSystems.00280-19

Extensive Thioautotrophic Gill Endosymbiont Diversity within a Single <i>Ctena orbiculata</i> (Bivalvia: Lucinidae) Population and Implications for Defining Host-Symbiont Specificity and Species Recognition
Cited by: 7
Author(s): Shen Jean Lim, Louie C. Alexander, Annette Summers Engel, Audrey Paterson, Laurie C. Anderson, Barbara J. Campbell
Software Mentions: 7
Published: over 5 years ago

10.1186/s13059-018-1438-9

UMI-count modeling and differential expression analysis for single-cell RNA sequencing
Cited by: 80
Author(s): Wenan Chen, Yán Li, John Easton, David Finkelstein, Gang Wu, Xiang Chen
Software Mentions: 7
Published: over 6 years ago

10.3389/fgene.2017.00062

Single-Cell RNA-Sequencing: Assessment of Differential Expression Analysis Methods
Cited by: 92
Author(s): Alessandra Dal Molin, Giacomo Baruzzo, Barbara Di Camillo
Software Mentions: 7
Published: over 7 years ago

10.1186/s12864-019-5686-1

aFold – using polynomial uncertainty modelling for differential gene expression estimation from RNA sequencing data
Cited by: 4
Author(s): Wentao Yang, Philip Rosenstiel, Hinrich Schulenburg
Software Mentions: 6
Published: over 5 years ago

10.1074/mcp.TIR119.001646

DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis
Cited by: 109
Author(s): Yong Zhu, Lukas M. Orre, Yan Zhou Tran, Georgios Mermelekas, Henrik J. Johansson, Alina Malyutina, Simon Anders, Janne Lehtiö
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.41556

Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase
Cited by: 40
Author(s): Sven Schenk, Stephanie Bannister, Fritz J. Sedlazeck, Dorothea Anrather, Bùi Quang Minh, Andrea Bileck, Markus Hartl, Arndt von Haeseler, Christopher Gerner, Florian Raible, Kristin Tessmar-Raible
Software Mentions: 5
Published: almost 6 years ago

10.1093/bib/bbv049

Empirical comparison of structure-based pathway methods
Cited by: 24
Author(s): Maria K. Jaakkola, Laura L. Elo
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-017-05949-y

Enhanced differential expression statistics for data-independent acquisition proteomics
Cited by: 29
Author(s): Tomi Suomi, Laura L. Elo
Software Mentions: 4
Published: over 7 years ago

10.1111/pbi.12898

A <i>Vitis vinifera</i> basic helix–loop–helix transcription factor enhances plant cell size, vegetative biomass and reproductive yield
Cited by: 34
Author(s): Sung Don Lim, Won Cheol Yim, Degao Liu, Rongbin Hu, Xiaohan Yang, John C. Cushman
Software Mentions: 4
Published: over 6 years ago

10.1093/bib/bbw057

Comparison of methods to detect differentially expressed genes between single-cell populations
Cited by: 73
Author(s): Maria K. Jaakkola, Fatemeh Seyednasrollah, Arfa Mehmood, Laura L. Elo
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0219551

Density distribution of gene expression profiles and evaluation of using maximal information coefficient to identify differentially expressed genes
Cited by: 16
Author(s): Han-Ming Liu, Dan Yang, Zhao-Fa Liu, Shengzhou Hu, Yan Shen-hai, Xian-Wen He
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-35218-5

Machine learning based classification of cells into chronological stages using single-cell transcriptomics
Cited by: 16
Author(s): Sumeet Pal Singh, Sharan Janjuha, Samata Chaudhuri, Susanne Reinhardt, Annekathrin Kränkel, Sevina Dietz, Anne Eugster, Halil I. Bilgin, Selçuk Korkmaz, Gökmen Zararsız, Nikolay Ninov, John E. Reid
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pcbi.1005562

ROTS: An R package for reproducibility-optimized statistical testing
Cited by: 98
Author(s): Tomi Suomi, Fatemeh Seyednasrollah, Maria K. Jaakkola, Thomas Faux, Laura L. Elo
Software Mentions: 2
Published: over 7 years ago

10.1093/bib/bbw095

A systematic evaluation of normalization methods in quantitative label-free proteomics
Cited by: 147
Author(s): Tommi Välikangas, Tomi Suomi, Laura L. Elo
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pmed.1003282

Mediterranean diet and endothelial function in patients with coronary heart disease: An analysis of the CORDIOPREV randomized controlled trial
Cited by: 69
Author(s): Elena M. Yubero‐Serrano, Carolina Fernández-Gandara, Antonio García‐Rios, Oriol A. Rangel‐Zúñiga, Francisco M. Gutiérrez-Mariscal, José D. Torres-Peña, Carmen Marı́n, Javier López-Moreno, Justo P. Castaño, Javier Delgado-Lista, José M. Ordovás, Pablo Pérez-Martínez, José López‐Miranda
Software Mentions: 1
Published: over 4 years ago

10.3389/fneur.2018.00407

Cerebrospinal Fluid Concentrations of Neuronal Proteins Are Reduced in Primary Angiitis of the Central Nervous System
Cited by: 13
Author(s): Tillmann Ruland, Jolien Wolbert, Michael G. Gottschalk, Simone König, Andreas Schulte‐Mecklenbeck, Jens Minnerup, Sven G. Meuth, Catharina C. Groß, Heinz Wiendl, Gerd Meyer zu Hörste
Software Mentions: 1
Published: over 6 years ago

10.1186/s41927-020-00122-x

Characterization of the interleukin-17 effect on articular cartilage in a translational model: an explorative study
Cited by: 15
Author(s): Dovilė Sinkevičiūtė, Anders Aspberg, Yi He, Anne‐Christine Bay‐Jensen, Patrik Önnerfjord
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0221509

A comparative proteomic study of plasma in Colombian childhood acute lymphoblastic leukemia
Cited by: 6
Author(s): Sandra Isabel Calderón-Rodríguez, María Carolina Sanabria‐Salas, Adriana Umaña‐Pérez
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22084082

Sigma-1 Receptor (S1R) Interaction with Cholesterol: Mechanisms of S1R Activation and Its Role in Neurodegenerative Diseases
Cited by: 22
Author(s): Vladimir Zhemkov, Michal Geva, Michael R. Hayden, Ilya Bezprozvanny
Software Mentions: 1
Published: over 3 years ago