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: cran: GRAPE

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/GRAPE

Gene-Ranking Analysis of Pathway Expression
2 versions
Latest release: over 5 years ago
150 downloads last month

Papers Mentioning GRAPE 24

A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments
Cited by: 49
Author(s): Mikel Esnaola, Pedro Puig, David Herrera González, Robert Castelo, Juan R. González
Software Mentions: 9
Published: about 11 years ago

10.1186/s12859-017-1711-z

GRAPE: a pathway template method to characterize tissue-specific functionality from gene expression profiles
Cited by: 8
Author(s): Michael Klein, David F. Stern, Hongyu Zhao
Software Mentions: 7
Published: about 7 years ago

10.1098/rstb.2010.0127

Competition for land
Cited by: 406
Author(s): Pete Smith, P. J. Gregory, Detlef van Vuuren, Michael Obersteiner, Petr Havlík, Mark Rounsevell, Jeremy Woods, Elke Stehfest, Jessica Bellarby
Software Mentions: 5
Published: almost 14 years ago

10.1093/bioinformatics/btt016

Grape RNA-Seq analysis pipeline environment
Cited by: 28
Author(s): David G. Knowles, Maik Röder, Angelika Merkel, Roderic Guigó
Software Mentions: 5
Published: over 11 years ago

10.3389/fdata.2021.693869

TSI-GNN: Extending Graph Neural Networks to Handle Missing Data in Temporal Settings
Cited by: 3
Author(s): D. Benjamin Gordon, Panayiotis Petousis, Henry Zheng, Davina Zamanzadeh, Alex A. T. Bui
Software Mentions: 4
Published: about 3 years ago

10.1155/2018/2046269

Instant Feedback Rapid Prototyping for GPU-Accelerated Computation, Manipulation, and Visualization of Multidimensional Data
Cited by: 1
Author(s): Maximilian Malek, Christoph Wilhelm Sensen
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.0030054

Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction
Cited by: 87
Author(s): Axel Bernal, Koby Crammer, Artemis G. Hatzigeorgiou, Fernando Pereira
Software Mentions: 3
Published: over 17 years ago

10.1089/cmb.2019.0286

More Accurate Transcript Assembly via Parameter Advising
Cited by: 4
Author(s): Dan DeBlasio, Kwanho Kim, Carl Kingsford
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0227032

FlexGraph: Flexible partitioning and storage for scalable graph mining
Cited by: 4
Author(s): Chiwan Park, Ha-Myung Park, U Kang
Software Mentions: 3
Published: over 4 years ago

10.1007/s10584-019-02539-x

Biomass residues as twenty-first century bioenergy feedstock—a comparison of eight integrated assessment models
Cited by: 28
Author(s): Steef V. Hanssen, Vassilis Daioglou, Zoran J. N. Steinmann, Stefan Frank, Alexander Popp, Thierry Brunelle, Pekka Lauri, Tomoko Hasegawa, Mark A. J. Huijbregts, Detlef P. van Vuuren
Software Mentions: 3
Published: about 5 years ago

10.1186/s13321-019-0335-x

rBAN: retro-biosynthetic analysis of nonribosomal peptides
Cited by: 15
Author(s): Emma Ricart, Valérie Leclère, Areski Flissi, Markus Mueller, Maude Pupin, Frédérique Lisacek
Software Mentions: 2
Published: over 5 years ago

10.1007/s11625-017-0521-6

Assessment of mitigation strategies as tools for risk management under future uncertainties: a multi-model approach
Cited by: 10
Author(s): Shunsuke Mori, Toyoaki Washida, Atsushi Kurosawa, Toshihiko Masui
Software Mentions: 2
Published: over 6 years ago

10.1098/rsta.2013.0387

MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations
Cited by: 64
Author(s): Itta Ohmura, Gentaro Morimoto, Yosuke Ohno, Aki Hasegawa, Makoto Taiji
Software Mentions: 2
Published: about 10 years ago

10.1038/srep41544

Discovery of Cancer Driver Long Noncoding RNAs across 1112 Tumour Genomes: New Candidates and Distinguishing Features
Cited by: 90
Author(s): Andrés Lanzós, Joana Carlevaro-Fita, Loris Mularoni, Ferrán Reverter, Emilio Palumbo, Roderic Guigó, Rory Johnson
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2019.03084

The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach
Cited by: 50
Author(s): Shane O’Donnell, R. Paul Ross, Catherine Stanton
Software Mentions: 2
Published: over 4 years ago

10.1007/s41114-018-0013-8

Relativistic dynamics and extreme mass ratio inspirals
Cited by: 86
Author(s): Pau Amaro-Seoane
Software Mentions: 1
Published: over 6 years ago

10.1093/bib/bbx146

Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters
Cited by: 104
Author(s): Kai Blin, Hyun Uk Kim, Marnix H. Medema, Tilmann Weber
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-018-4435-1

Global analysis of prokaryotic tRNA-derived cyclodipeptide biosynthesis
Cited by: 25
Author(s): Michael A. Skinnider, Chad W. Johnston, Nishanth J. Merwin, Chris A. Dejong, Nathan A. Magarvey
Software Mentions: 1
Published: over 6 years ago

10.1186/s13321-017-0234-y

Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm
Cited by: 29
Author(s): Michael A. Skinnider, Chris A. Dejong, Brian C. Franczak, Paul D. McNicholas, Nathan A. Magarvey
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-020-80070-1

Hybrid quantum-classical approach to enhanced quantum metrology
Cited by: 6
Author(s): Xiaodong Yang, Xi Chen, Jun Li, Xinhua Peng, Raymond Laflamme
Software Mentions: 1
Published: over 3 years ago

10.1007/s11625-018-0530-0

Risk implications of long-term global climate goals: overall conclusions of the ICA-RUS project
Cited by: 9
Author(s): Seita Emori, Kiyoshi Toko, Yoshiki Yamagata, Shinjiro Kanae, Shunsuke Mori, Yuko Fujigaki
Software Mentions: 1
Published: over 6 years ago

10.3390/nu4121945

Grape Consumption Increases Anti-Inflammatory Markers and Upregulates Peripheral Nitric Oxide Synthase in the Absence of Dyslipidemias in Men with Metabolic Syndrome
Cited by: 39
Author(s): Jacqueline Barona, Christopher N. Blesso, Catherine J. Andersen, Youngki Park, Jiyoung Lee, María Luz Fernández
Software Mentions: 1
Published: almost 12 years ago

10.3390/ijerph18073351

Koshu GRoup Activity, Active Play and Exercise (GRAPE) Study: A Cluster Randomised Controlled Trial Protocol of a School-Based Intervention among Japanese Children
Cited by: 0
Author(s): Mitsuya Yamakita, Daisuke Ando, Hayato Sugita, Yuka Akiyama, Mitsuaki Sato, Hiroshi Yokomichi, Kaori Yamaguchi, Zentaro Yamagata
Software Mentions: 1
Published: over 3 years ago

10.3390/ma11050675

Effects of Pre-Treatments on Bioactivity of High-Purity Titanium
Cited by: 3
Author(s): Yaming Wang, Guangxin Wang, Zhi Lü, Wuhui Li, Yanfu Yan, Yongfa Song, Akiyoshi Osaka
Software Mentions: 1
Published: over 6 years ago