cran: Rcpp | Projects | Ecosyste.ms: Papers

10.1111/jam.14807

Validation of the bag‐mediated filtration system for environmental surveillance of poliovirus in Nairobi, Kenya
Cited by: 3
Author(s): Christine S. Fagnant-Sperati, You Ren, Nicolette A. Zhou, Evans Komen, Benlick Mwangi, Joanne Hassan, Agnes Chepkurui, Rosemary Nzunza, James Nyangao, Walda B. van Zyl, Marianne Wolfaardt, Peter N. Matsapola, Fhatuwani B. Ngwana, Stacey Jeffries-Miles, Angela Coulliette-Salmond, Silvia Peñaranda, Everardo Vega, Jeffry H. Shirai, Alexandra L. Kossik, Nicola K. Beck, D S Boyle, Cara C. Burns, Maureen B. Taylor, Peter Borus, John Scott Meschke
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-016-1300-6

AlignStat: a web-tool and R package for statistical comparison of alternative multiple sequence alignments
Cited by: 9
Author(s): Thomas Shafee, Ira Cooke
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-28701-6

Reconciling differences in natural tags to infer demographic and genetic connectivity in marine fish populations
Cited by: 30
Author(s): Ruth Patrick, Susanne E. Tanner, Maria Ana Aboim, Rita P. Vasconcelos, Jean Laroche, Grégory Charrier, Montse Pérez, Pablo Presa, Bronwyn M. Gillanders, Henrique N. Cabral
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-14-688

Guide: a desktop application for analysing gene expression data
Cited by: 5
Author(s): Jarny Choi
Software Mentions: 3
Published: almost 12 years ago

10.21105/joss.00860

TDAstats: R pipeline for computing persistent homology in topological data analysis
Cited by: 22
Author(s): Raoul Wadhwa, Drew F. K. Williamson, Andrew Dhawan, Jacob G. Scott
Software Mentions: 3
Published: over 6 years ago

10.1128/mSphere.00191-21

Amplicon Sequence Variants Artificially Split Bacterial Genomes into Separate Clusters
Cited by: 61
Author(s): Patrick D. Schloss
Software Mentions: 3
Published: about 3 years ago

10.1186/s12938-016-0305-8

Probabilistic liver atlas construction
Cited by: 9
Author(s): Estrella Durá, Juan Carlos Ureta Domingo, Guillermo Ayala, Luis Martí‐Bonmatí, Evgin Göçeri
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12859-017-1583-2

microclass: an R-package for 16S taxonomy classification
Cited by: 17
Author(s): Kristian Hovde Liland, Hilde Vinje, Lars-Gustav Snipen
Software Mentions: 3
Published: over 7 years ago

10.3390/genes12020185

Graph Algorithms for Mixture Interpretation
Cited by: 4
Author(s): Benjamin Crysup, August E. Woerner, Jonathan L. King, Bruce Budowle
Software Mentions: 3
Published: almost 4 years ago

10.1007/s11336-018-9648-3

A Simple Method for Comparing Complex Models: Bayesian Model Comparison for Hierarchical Multinomial Processing Tree Models Using Warp-III Bridge Sampling
Cited by: 20
Author(s): Quentin Frederik Gronau, Eric–Jan Wagenmakers, Daniel W. Heck, Dora Matzke
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12876-021-01714-8

Plasma cell free DNA methylation markers for hepatocellular carcinoma surveillance in patients with cirrhosis: a case control study
Cited by: 11
Author(s): Jörn Lewin, Denise Kottwitz, Johanna Aoyama, Theo deVos, J. Garces, Oliver Hasinger, Stefanie Kasielke, Florian Knaust, Preeti Rathi, Sebastian Rausch, Günter Weiß, Alexander Zipprich, Edward Mena, Tse‐Ling Fong
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-016-1244-x

rapidGSEA: Speeding up gene set enrichment analysis on multi-core CPUs and CUDA-enabled GPUs
Cited by: 1
Author(s): Christian Hundt, Andreas Hildebrandt, Bertil Schmidt
Software Mentions: 2
Published: about 8 years ago

10.1186/s12859-015-0598-9

MANTIS: an R package that simulates multilocus models of pathogen evolution
Cited by: 10
Author(s): José Lourenço, Paul S. Wikramaratna, Sunetra Gupta
Software Mentions: 2
Published: over 9 years ago

10.1093/ije/dyy012

Longitudinal analysis strategies for modelling epigenetic trajectories
Cited by: 10
Author(s): James R Staley, Matthew Suderman, Andrew Simpkin, Tom R. Gaunt, Jon Heron, Caroline L Relton, Kate Tilling
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pcbi.1006935

CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer
Cited by: 3
Author(s): Thomas D. Sherman, Luciane T. Kagohara, Raymon Cao, Raymond Cheng, Matthew Satriano, Michael Considine, Gabriel Krigsfeld, Ruchira S. Ranaweera, Yong Tang, Sandra A. Jablonski, Genevieve Stein-O’Brien, Daria A. Gaykalova, Louis M. Weiner, Christine H. Chung, Elana J. Fertig
Software Mentions: 2
Published: over 5 years ago

10.1016/j.epidem.2021.100460

Competition between RSV and influenza: Limits of modelling inference from surveillance data
Cited by: 9
Author(s): Naomi R. Waterlow, Stefan Flasche, Amanda Minter, Rosalind M Eggo
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pbio.2004974

Timescales of influenza A/H3N2 antibody dynamics
Cited by: 39
Author(s): Adam J. Kucharski, Justin Lessler, Derek A. T. Cummings, Steven Riley
Software Mentions: 2
Published: over 6 years ago

10.3389/fbioe.2020.00607

High-Throughput Screen for Cell Wall Synthesis Network Module in Mycobacterium tuberculosis Based on Integrated Bioinformatics Strategy
Cited by: 1
Author(s): Xizi Luo, Jiahui Pan, Qingyu Meng, Juanjuan Huang, Wenfang Wang, Nan Zhang, Guoqing Wang
Software Mentions: 2
Published: over 4 years ago

10.1186/s12985-017-0778-5

Molecular epidemiology of Avian Rotaviruses Group A and D shed by different bird species in Nigeria
Cited by: 19
Author(s): Maude Pauly, O.O. Oni, Aurélie Sausy, A. A. Owoade, C. A. O. Adeyefa, Claude P. Muller, Judith M. Hübschen, Chantal J. Snoeck
Software Mentions: 2
Published: over 7 years ago

10.1007/s00285-017-1100-2

Oscillating systems with cointegrated phase processes
Cited by: 7
Author(s): Jacob Østergaard, Anders Rahbek, Susanne Ditlevsen
Software Mentions: 2
Published: almost 8 years ago

10.1007/s11306-017-1178-y

NMRProcFlow: a graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics
Cited by: 112
Author(s): Daniel Jacob, Catherine Deborde, Marie Lefebvre, Mickaël Maucourt, Annick Moing
Software Mentions: 2
Published: almost 8 years ago

10.1002/mrm.25723

Microstructural parameter estimation in vivo using diffusion MRI and structured prior information
Cited by: 12
Author(s): Jonathan D. Clayden, Zoltán Nagy, Nikolaus Weiskopf, Daniel C. Alexander, Chris A. Clark
Software Mentions: 2
Published: over 9 years ago

10.1016/S2352-3018(20)30315-5

Trends in knowledge of HIV status and efficiency of HIV testing services in sub-Saharan Africa, 2000–20: a modelling study using survey and HIV testing programme data
Cited by: 59
Author(s): Katia Giguère, Jeffrey W. Eaton, Kimberly Marsh, Leigh F. Johnson, Cheryl Johnson, E. Ehui, Andreas Jahn, Ian Wanyeki, Francisco Mbofana, Fidèle Bakiono, Mary Mahy, Mathieu Maheu‐Giroux
Software Mentions: 2
Published: over 3 years ago

10.1534/g3.116.032359

A Genomic Bayesian Multi-trait and Multi-environment Model
Cited by: 105
Author(s): Osval A. Montesinos-L֯ópez, Abelardo Montesinos‐López, José Crossa, Fernando H. Toledo, Óscar Pérez-Hernández, Kent M. Eskridge, Jessica Rutkoski
Software Mentions: 2
Published: about 8 years ago

10.1534/g3.116.038612

Time-Variant Genetic Effects as a Cause for Preterm Birth: Insights from a Population of Maternal Cousins in Sweden
Cited by: 6
Author(s): Julius Juodakis, Jonas Bacelis, Ge Zhang, Louis J. Muglia, Bo Jacobsson
Software Mentions: 2
Published: over 7 years ago

10.1093/bioinformatics/btaa199

Estimation of dynamic SNP-heritability with Bayesian Gaussian process models
Cited by: 5
Author(s): Arttu Arjas, Andreas Hauptmann, Mikko J. Sillanpää
Software Mentions: 2
Published: over 4 years ago

10.1186/s13059-015-0708-z

Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome
Cited by: 86
Author(s): Alessandro Mammana, Ho‐Ryun Chung
Software Mentions: 2
Published: over 9 years ago

10.1093/bioinformatics/btx206

RTK: efficient rarefaction analysis of large datasets
Cited by: 74
Author(s): Paul Saary, Kristoffer Forslund, Peer Bork, Falk Hildebrand
Software Mentions: 2
Published: over 7 years ago

10.1186/s13059-021-02404-0

SPARK-X: non-parametric modeling enables scalable and robust detection of spatial expression patterns for large spatial transcriptomic studies
Cited by: 69
Author(s): Jiaqiang Zhu, Shuang Sun, Xiang Zhou
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-019-3312-5

Optimization and expansion of non-negative matrix factorization
Cited by: 51
Author(s): Xihui Lin, Paul C. Boutros
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12859-018-2310-3

cuRnet: an R package for graph traversing on GPU
Cited by: 4
Author(s): Vincenzo Bonnici, Federico Busato, Stefano Aldegheri, Murodzhon Akhmedov, Luciano Cascione, Alberto Arribas Carmena, Francesco Bertoni, Nicola Bombieri, Ivo Kwee, Rosalba Giugno
Software Mentions: 2
Published: about 6 years ago

10.1186/s12859-020-03640-0

MicroBVS: Dirichlet-tree multinomial regression models with Bayesian variable selection - an R package
Cited by: 6
Author(s): Matthew D. Koslovsky, Marina Vannucci
Software Mentions: 2
Published: over 4 years ago

10.1007/s11222-019-09909-6

Spectral density-based and measure-preserving ABC for partially observed diffusion processes. An illustration on Hamiltonian SDEs
Cited by: 13
Author(s): Evelyn Buckwar, Massimiliano Tamborrino, Irene Tubikanec
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0179143

Transcriptional mechanisms associated with seed dormancy and dormancy loss in the gibberellin-insensitive sly1-2 mutant of Arabidopsis thaliana
Cited by: 13
Author(s): Sven K. Nelson, Camille M. Steber
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0222664

Direct estimation of the parameters of a delayed, intermittent activation feedback model of postural sway during quiet standing
Cited by: 13
Author(s): Kevin L. McKee, Michael C. Neale
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pmed.1002664

Expected changes in obesity after reformulation to reduce added sugars in beverages: A modeling study
Cited by: 28
Author(s): Ana Basto-Abreu, Ariela Braverman-Bronstein, Dalia Camacho‐García‐Formentí, Rodrigo Zepeda-Tello, Barry M. Popkin, Juan Rivera‐Dommarco, Mauricio Hernández-Ávila, Tonatiuh Barrientos‐Gutiérrez
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pgen.1007774

How many individuals share a mitochondrial genome?
Cited by: 19
Author(s): Mikkel Meyer Andersen, David J. Balding
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pcbi.1006425

Understanding narwhal diving behaviour using Hidden Markov Models with dependent state distributions and long range dependence
Cited by: 16
Author(s): Mạnh Cường Ngô, Mads Peter Heide‐Jørgensen, Susanne Ditlevsen
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1004333

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data
Cited by: 255
Author(s): Catalina A. Vallejos, John C. Marioni, Sylvia Richardson
Software Mentions: 2
Published: over 9 years ago

10.1002/ece3.5448

Analysis of interval‐grouped data in weed science: The binnednp Rcpp package
Cited by: 4
Author(s): Daniel Barreiro‐Ures, Mario Francisco‐Fernández, Ricardo Cao, Basilio B. Fraguela, David Deibe, José Luis González‐Andújar, Miguel Reyes
Software Mentions: 2
Published: about 5 years ago

10.3390/s21113705

On the Achievable Max-Min User Rates in Multi-Carrier Centralized NOMA-VLC Networks
Cited by: 1
Author(s): Omar Maraqa, Umair F. Siddiqi, Saad Al-Ahmadi, Sadiq M. Sait
Software Mentions: 1
Published: over 3 years ago

10.1093/biostatistics/kxy024

A Bayesian space–time model for clustering areal units based on their disease trends
Cited by: 12
Author(s): Gary Napier, Duncan Lee, Chris Robertson, Andrew Lawson
Software Mentions: 1
Published: over 6 years ago

10.1186/s12859-019-2882-6

metaSPARSim: a 16S rRNA gene sequencing count data simulator
Cited by: 15
Author(s): Ilaria Patuzzi, Giacomo Baruzzo, Carmen Losasso, Antonia Ricci, Barbara Di Camillo
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2156-13-100

A comparison of statistical methods for genomic selection in a mice population
Cited by: 61
Author(s): Haroldo Henrique de Rezende Neves, Roberto Carvalheiro, Salete Linhares Queiroz
Software Mentions: 1
Published: almost 13 years ago

10.1098/rsif.2021.0362

Estimating parameters of a stochastic cell invasion model with fluorescent cell cycle labelling using approximate Bayesian computation
Cited by: 7
Author(s): Michael J. Carr, Matthew J. Simpson, Christopher Drovandi
Software Mentions: 1
Published: about 3 years ago

10.1534/g3.119.400335

micRocounter: Microsatellite Characterization in Genome Assemblies
Cited by: 1
Author(s): Johnathan Lo, Michelle M. Jonika, Heath Blackmon
Software Mentions: 1
Published: about 5 years ago

10.1186/s12874-019-0725-9

A Bayesian multivariate latent t-regression model for assessing the association between corticosteroid and cranial radiation exposures and cardiometabolic complications in survivors of childhood acute lymphoblastic leukemia: a PETALE study
Cited by: 3
Author(s): Miguel Caubet Fernandez, Simon Drouin, Mariia Samoilenko, Sylvie Morel, Maja Krajinović, Caroline Laverdière, Daniel Sinnett, Émile Lévy, Valérie Marcil, Geneviève Lefebvre
Software Mentions: 1
Published: over 5 years ago

10.1186/s12889-015-2235-y

A dengue outbreak on a floating village at Cat Ba Island in Vietnam
Cited by: 11
Author(s): Thanh Le Viet, Marc Choisy, Juliet E. Bryant, Duoc Vu Trong, Thai Pham Quang, Peter Horby, Hien Nguyen Tran, Huong Tran Thi Kieu, Trung Nguyen Vu, Kính Nguyen Văn, Mai Le Thi Quynh, Heiman Wertheim
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-020-65313-5

A biomathematical model of human erythropoiesis and iron metabolism
Cited by: 4
Author(s): Sibylle Schirm, Markus Scholz
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pcbi.1005382

Human mobility and the spatial transmission of influenza in the United States
Cited by: 160
Author(s): Vivek Charu, Scott L. Zeger, Julia R. Gog, Ottar N. Bjørnstad, Stephen M Kissler, Lone Simonsen, Bryan T. Grenfell, Cécile Viboud
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12859-016-1181-8

Interpreting transcriptional changes using causal graphs: new methods and their practical utility on public networks
Cited by: 28
Author(s): Carl Tony Fakhry, Parul Choudhary, Alex Gutteridge, Ben S. Sidders, Ping Chen, Daniel Ziemek, Kourosh Zarringhalam
Software Mentions: 1
Published: over 8 years ago

10.3390/s20247194

Automatic Detection of Individual Trees from VHR Satellite Images Using Scale-Space Methods
Cited by: 3
Author(s): Milad Mahour, V.A. Tolpekin, Alfred Stein
Software Mentions: 1
Published: almost 4 years ago

Projects: cran: Rcpp

Papers Mentioning Rcpp 152