cran: foreach | Projects | Ecosyste.ms: Papers

10.1186/1471-2156-15-81

Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations
Cited by: 16
Author(s): Robert B. Scharpf, Lynn Mireles, Qiong Yang, Anna Köttgen, Ingo Ruczinski, Katalin Suszták, Eitan Halper-Stromberg, Adrienne Tin, Stephen Cristiano, Aravinda Chakravarti, Eric Boerwinkle, Caroline S. Fox, Josef Coresh, W. H. Linda Kao
Software Mentions: 56
Published: almost 11 years ago

10.7717/peerj-cs.175

Software engineering principles to improve quality and performance of R software
Cited by: 0
Author(s): Seth Russell, Tellen D. Bennett, Debashis Ghosh
Software Mentions: 29
Published: almost 6 years ago

10.3389/fmolb.2020.570702

Prognostic Prediction Using a Stemness Index-Related Signature in a Cohort of Gastric Cancer
Cited by: 27
Author(s): Xiaowei Chen, Dawei Zhang, Fei Jiang, Yan Shen, Xin Li, Xin Hu, Pingmin Wei, Xiaobing Shen
Software Mentions: 24
Published: over 4 years ago

10.3390/genes11030257

mRNAsi Index: Machine Learning in Mining Lung Adenocarcinoma Stem Cell Biomarkers
Cited by: 61
Author(s): Yitong Zhang, Joseph T. Tseng, I-Chia Lien, Fenglan Li, Wei Wu, Hui Li
Software Mentions: 20
Published: almost 5 years ago

10.1371/journal.pone.0061217

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
Cited by: 11,386
Author(s): Paul J. McMurdie, Susan Holmes
Software Mentions: 19
Published: over 11 years ago

10.1371/journal.pone.0195970

The importance of regional models in assessing canine cancer incidences in Switzerland
Cited by: 4
Author(s): Gianluca Boo, Stefan Leyk, Chris Brunsdon, Ricarda Graf, Andreas Pospischil, Sara Irina Fabrikant
Software Mentions: 18
Published: over 6 years ago

10.1186/s13059-021-02295-1

gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models
Cited by: 77
Author(s): Johannes Zimmermann, Christoph Kaleta, Silvio Waschina
Software Mentions: 18
Published: almost 4 years ago

10.1371/journal.pcbi.1003531

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
Cited by: 2,083
Author(s): Paul J. McMurdie, Susan Holmes
Software Mentions: 17
Published: over 10 years ago

10.3389/fimmu.2021.668391

A Transcriptional Signature of PDGF-DD Activated Natural Killer Cells Predicts More Favorable Prognosis in Low-Grade Glioma
Cited by: 21
Author(s): Yuhan Sun, Alexander James Sedgwick, Yaseelan Palarasah, Stefano Mangiola, Alexander D. Barrow
Software Mentions: 15
Published: over 3 years ago

10.1186/s12859-020-03860-4

Finding a suitable library size to call variants in RNA-Seq
Cited by: 3
Author(s): Anna Quaglieri, Christoffer Flensburg, Terence P. Speed, Ian J. Majewski
Software Mentions: 15
Published: about 4 years ago

10.1371/journal.pgen.1009110

Unique genetic signatures of local adaptation over space and time for diapause, an ecologically relevant complex trait, in Drosophila melanogaster
Cited by: 45
Author(s): Priscilla A. Erickson, Cory A. Weller, Daniel Song, Alyssa Bangerter, Paul S. Schmidt, Alan O. Bergland
Software Mentions: 15
Published: about 4 years ago

10.1371/journal.pcbi.1005158

Machine Learning for Characterization of Insect Vector Feeding
Cited by: 25
Author(s): Denis S. Willett, Justin George, Nora S. Willett, Lukasz L. Stelinski, Stephen L. Lapointe
Software Mentions: 14
Published: about 8 years ago

10.3389/fmicb.2020.02033

Plasmid Interactions Can Improve Plasmid Persistence in Bacterial Populations
Cited by: 24
Author(s): João Alves Gama, Rita Zilhão, Francisco Dionísio
Software Mentions: 13
Published: over 4 years ago

10.1371/journal.pone.0212669

Batch adjustment by reference alignment (BARA): Improved prediction performance in biological test sets with batch effects
Cited by: 3
Author(s): Robin Gradin, Malin Lindstedt, Henrik J. Johansson
Software Mentions: 13
Published: almost 6 years ago

10.3389/fimmu.2021.730346

Nasal Immunization With Small Molecule Mast Cell Activators Enhance Immunity to Co-Administered Subunit Immunogens
Cited by: 6
Author(s): Brandi T. Johnson‐Weaver, Hae Woong Choi, Hui Yang, Joshua A. Granek, Cliburn Chan, Soman N. Abraham, Herman F. Staats
Software Mentions: 13
Published: over 3 years ago

10.3389/fmicb.2021.616013

Distribution of Bacterial Endophytes in the Non-lesion Tissues of Potato and Their Response to Potato Common Scab
Cited by: 7
Author(s): Wencong Shi, Gaoya Su, Mingcong Li, Bing Wang, Runmao Lin, Yang Yu-tian, Tao Wei, Bo Zhou, Zheng Gao
Software Mentions: 13
Published: almost 4 years ago

10.1186/s12919-016-0015-z

Analysis of gene expression to predict dynamics of future hypertension incidence in type 2 diabetic patients
Cited by: 8
Author(s): Piotr Radkowski, Gracjan Wątor, Jan Skupień, Anna Bogdali, Paweł Wołkow
Software Mentions: 12
Published: about 8 years ago

10.3389/fonc.2020.596822

Predictive Model and Precaution for Oral Mucositis During Chemo-Radiotherapy in Nasopharyngeal Carcinoma Patients
Cited by: 10
Author(s): Peijing Li, Kaixin Li, Tengchuan Jin, Hua Lin, Jun Fang, Shengchun Yang, Wei‐Chih Shen, Jia Chen, Jiang Zhang, Xiaozhong Chen, Ming Chen, Yuanyuan Chen
Software Mentions: 12
Published: about 4 years ago

10.1186/s13073-016-0384-y

XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits
Cited by: 131
Author(s): Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C. Knight
Software Mentions: 12
Published: about 8 years ago

10.1371/journal.pcbi.1003929

dcGOR: An R Package for Analysing Ontologies and Protein Domain Annotations
Cited by: 18
Author(s): Hai Fang
Software Mentions: 11
Published: about 10 years ago

10.1155/2016/7972351

Advancements in RNASeqGUI towards a Reproducible Analysis of RNA-Seq Experiments
Cited by: 11
Author(s): Francesco Russo, Dario Righelli, Claudia Angelini
Software Mentions: 11
Published: almost 9 years ago

10.1098/rspb.2021.0343

A multi-faceted comparative perspective on elevational beta-diversity: the patterns and their causes
Cited by: 17
Author(s): Yuanbao Du, Liqing Fan, Zaifu Xu, Zhixin Wen, Tianlong Cai, Anderson Feijó, Junhua Hu, Fumin Lei, Qisen Yang, Huijie Qiao
Software Mentions: 10
Published: over 3 years ago

10.1038/s41598-019-52520-y

Naturally-primed life strategy plasticity of dimorphic Aethionema arabicum facilitates optimal habitat colonization
Cited by: 14
Author(s): Samik Bhattacharya, Katja Sperber, Barış Özüdoğru, Gerhard Leubner‐Metzger, Klaus Mummenhoff
Software Mentions: 10
Published: about 5 years ago

10.3390/jintelligence6030030

The Relation of Personality and Intelligence—What Can the Brunswik Symmetry Principle Tell Us?
Cited by: 80
Author(s): André Kretzschmar, Marion Spengler, Anna‐Lena Schubert, Ricarda Steinmayr, Matthias Ziegler
Software Mentions: 9
Published: over 6 years ago

10.1186/s12859-020-3463-4

ORdensity: user-friendly R package to identify differentially expressed genes
Cited by: 0
Author(s): José María Martínez-Otzeta, Itziar Irigoien, Basilio Sierra, C. Arenas
Software Mentions: 9
Published: over 4 years ago

10.1371/journal.pcbi.1008742

Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes
Cited by: 11
Author(s): Johannes Asplund-Samuelsson, Elton P. Hudson
Software Mentions: 9
Published: almost 4 years ago

10.1371/journal.ppat.1009068

Modeling intra-mosquito dynamics of Zika virus and its dose-dependence confirms the low epidemic potential of Aedes albopictus
Cited by: 16
Author(s): Sébastian Lequime, Jean-Sébastien Dehecq, Séverine Matheus, Franck de Laval, Lionel Alméras, Sébastien Briolant, Albin Fontaine
Software Mentions: 9
Published: almost 4 years ago

10.1111/2041-210X.12490

hext , a software supporting tree‐based screens for hybrid taxa in multilocus data sets, and an evaluation of the homoplasy excess test
Cited by: 4
Author(s): Kevin Schneider, Stephan Koblmüller, Kristina M. Sefc
Software Mentions: 8
Published: about 9 years ago

10.1038/s41598-017-11110-6

A Novel Statistical Method to Diagnose, Quantify and Correct Batch Effects in Genomic Studies
Cited by: 29
Author(s): Gift Nyamundanda, Pawan Poudel, Yatish Patil, Anguraj Sadanandam
Software Mentions: 8
Published: over 7 years ago

10.4056/sigs.3377516

Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron.
Cited by: 8
Author(s): Kristen M. DeAngelis, Patrik D’haeseleer, Dylan Chivian, Blake A. Simmons, Adam P. Arkin, Konstantinos Mavromatis, Stephanie Malfatti, Susannah G. Tringe, Terry C. Hazen
Software Mentions: 7
Published: almost 12 years ago

10.1111/1556-4029.14482

Getting Rid of Dichotomous Sex Estimations: Why Logistic Regression Should be Preferred Over Discriminant Function Analysis
Cited by: 13
Author(s): Björn Bartholdy, Elena Sandoval, Menno L. P. Hoogland, Sarah Schrader
Software Mentions: 6
Published: over 4 years ago

10.1186/s12954-019-0289-3

Prevalence of injecting drug use in Estonia 2010–2015: a capture-recapture study
Cited by: 6
Author(s): Mait Raag, Sigrid Vorobjov, Anneli Uusküla
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0243208

Two-stage topic modelling of scientific publications: A case study of University of Nairobi, Kenya
Cited by: 16
Author(s): Leacky K Muchene, Wende Clarence Safari
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.ppat.1007187

Epidemiological significance of dengue virus genetic variation in mosquito infection dynamics
Cited by: 39
Author(s): Albin Fontaine, Sébastian Lequime, Isabelle Moltini-Conclois, Davy Jiolle, Isabelle Leparc-Goffart, Robert C. Reiner, Louis Lambrechts
Software Mentions: 6
Published: over 6 years ago

10.1002/ece3.5887

Phenotypic plasticity, but not adaptive tracking, underlies seasonal variation in post‐cold hardening freeze tolerance of<i>Drosophila melanogaster</i>
Cited by: 9
Author(s): Helen M. Stone, Priscilla A. Erickson, Alan O. Bergland
Software Mentions: 5
Published: about 5 years ago

10.3389/fcell.2014.00040

Quantifying periodicity in omics data
Cited by: 7
Author(s): Cornelia Amariei, Masaru Tomita, Douglas B. Murray
Software Mentions: 5
Published: over 10 years ago

10.1038/s41598-020-62782-6

Exploring the configuration spaces of surface materials using time-dependent diffraction patterns and unsupervised learning
Cited by: 4
Author(s): Daniel M. Packwood
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0229052

Combined impact of pesticides and other environmental stressors on animal diversity in irrigation ponds
Cited by: 16
Author(s): Hiroshi C. Ito, Hiroaki Shiraishi, Megumi Nakagawa, Noriko Takamura
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pntd.0005701

The interplay of climate, intervention and imported cases as determinants of the 2014 dengue outbreak in Guangzhou
Cited by: 30
Author(s): Qu Cheng, Qinlong Jing, Robert C. Spear, John M. Marshall, Zhicong Yang, Peng Gong
Software Mentions: 5
Published: over 7 years ago

10.1186/s12859-016-1228-x

The parameter sensitivity of random forests
Cited by: 91
Author(s): Barbara Huang, Paul C. Boutros
Software Mentions: 5
Published: over 8 years ago

10.1186/s12874-018-0574-y

Hypothesis testing in Bayesian network meta-analysis
Cited by: 12
Author(s): Lorenz Uhlmann, Katrin Jensen, Meinhard Kieser
Software Mentions: 5
Published: about 6 years ago

10.3389/fgene.2021.655638

Alternative Ways of Computing the Numerator Relationship Matrix
Cited by: 4
Author(s): Mohammad Ali Nilforooshan, Dorian J. Garrick, B. L. Harris
Software Mentions: 4
Published: over 3 years ago

10.1002/ece3.12

Ungulate preference for burned patches reveals strength of fire-grazing interaction
Cited by: 216
Author(s): Brady W. Allred, Samuel D. Fuhlendorf, David M. Engle, R. Dwayne Elmore
Software Mentions: 4
Published: over 13 years ago

10.3389/fphys.2018.01328

A Novel Data-Driven Boolean Model for Genetic Regulatory Networks
Cited by: 10
Author(s): Leshi Chen, Don Kulasiri, Sandhya Samarasinghe
Software Mentions: 4
Published: about 6 years ago

10.1186/s13072-017-0131-7

A computational approach for the functional classification of the epigenome
Cited by: 3
Author(s): Francesco Gandolfi, Anna Tramontano
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0236559

Understanding resource utilization and mortality in COPD to support policy making: A microsimulation study
Cited by: 0
Author(s): Elizabeth G. Bond, Lusine Abrahamyan, Mohammad Kaviul Anam Khan, Andrea S. Gershon, Murray Krahn, Ping Li, Rajibul Mian, Nicholas Mitsakakis, Mohsen Sadatsafavi, Teresa To, Petros Pechlivanoglou
Software Mentions: 3
Published: over 4 years ago

10.1186/1756-0381-4-24

An R package implementation of multifactor dimensionality reduction
Cited by: 25
Author(s): Stacey J. Winham, Alison A. Motsinger‐Reif
Software Mentions: 3
Published: over 13 years ago

10.1038/sdata.2016.69

Spatially-explicit models of global tree density
Cited by: 7
Author(s): Henry B. Glick, Charlie Bettigole, Daniel S. Maynard, Kristofer Covey, Jeffrey R. Smith, Thomas W. Crowther
Software Mentions: 3
Published: over 8 years ago

10.1186/s12898-019-0273-5

Species traits, patch turnover and successional dynamics: when does intermediate disturbance favour metapopulation occupancy?
Cited by: 3
Author(s): Frederico Mestre, Ricardo Pita, António Mira, Pedro Beja
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0153673

Improving the Spatial Prediction of Soil Organic Carbon Stocks in a Complex Tropical Mountain Landscape by Methodological Specifications in Machine Learning Approaches
Cited by: 60
Author(s): Mareike Ließ, Johannes Schmidt, Bruno Glaser
Software Mentions: 2
Published: over 8 years ago

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