cran: Rcpp | Projects | Ecosyste.ms: Papers

10.3390/metabo9100200

The metaRbolomics Toolbox in Bioconductor and beyond
Cited by: 61
Author(s): Jan Stanstrup, Corey D. Broeckling, Rick Helmus, Nils Hoffmann, Ewy A. Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Michael Rainer, Reza M. Salek, Tobias Schulze, Emma L. Schymanski, Michael A. Stravs, Etienne Thévenot, Hendrik Treutler, Ralf Weber, Egon Willighagen, Michael Witting, Steffen Neumann
Software Mentions: 92
Published: about 5 years ago

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

10.1371/journal.pcbi.1007912

bigPint: A Bioconductor visualization package that makes big data pint-sized
Cited by: 3
Author(s): Lindsay Rutter, Dianne Cook
Software Mentions: 47
Published: over 4 years ago

10.12688/f1000research.22259.1

Fluent genomics with plyranges and tximeta
Cited by: 2
Author(s): Stuart Lee, Michael C. Lawrence, Michael I. Love
Software Mentions: 35
Published: over 4 years ago

10.12688/f1000research.9973.2

BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
Cited by: 20
Author(s): Andrea Komljenović, Julien Roux, Julien Wollbrett, Marc Robinson‐Rechavi, Frederic Bastian
Software Mentions: 33
Published: about 6 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: over 5 years ago

10.1016/j.patter.2021.100322

The role of metadata in reproducible computational research
Cited by: 38
Author(s): Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Karthik Ram, Jane Greenberg
Software Mentions: 21
Published: about 3 years ago

10.1371/journal.pcbi.1006361

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data
Cited by: 92
Author(s): Tian Li, Shian Su, Xueyi Dong, Daniela Amann‐Zalcenstein, Christine Biben, Azadeh Seidi, Douglas J. Hilton, Shalin H. Naik, Matthew E. Ritchie
Software Mentions: 21
Published: about 6 years ago

10.1186/s13321-020-00477-w

patRoon: open source software platform for environmental mass spectrometry based non-target screening
Cited by: 76
Author(s): Rick Helmus, Thomas L. ter Laak, Annemarie P. van Wezel, P. de Voogt, Emma L. Schymanski
Software Mentions: 20
Published: over 3 years ago

10.1186/s12859-019-3152-3

flowEMMi: an automated model-based clustering tool for microbial cytometric data
Cited by: 16
Author(s): Joachim Ludwig, Christian Höner zu Siederdissen, Zishu Liu, Peter F. Stadler, Susann Müller
Software Mentions: 18
Published: almost 5 years ago

10.1038/s41598-021-88209-4

Identification of transcriptional subtypes in lung adenocarcinoma and squamous cell carcinoma through integrative analysis of microarray and RNA sequencing data
Cited by: 6
Author(s): François Fauteux, Anuradha Surendra, Scott McComb, Youlian Pan, Jonathan D. Hill
Software Mentions: 15
Published: over 3 years ago

10.1371/journal.pcbi.1008625

mbkmeans: Fast clustering for single cell data using mini-batch k-means
Cited by: 27
Author(s): Stephanie C. Hicks, Ruoxi Liu, Yuwei Ni, Elizabeth Purdom, Davide Risso
Software Mentions: 15
Published: over 3 years ago

10.1371/journal.ppat.1009637

A field test of the dilution effect hypothesis in four avian multi-host pathogens
Cited by: 11
Author(s): Martina Ferraguti, Josué Martínez‐de la Puente, Miguel Ángel Jiménez‐Clavero, Francisco Rubio Llorente, David Roiz, Santiago Ruíz, Ramón C. Soriguer, Jordi Figuerola
Software Mentions: 14
Published: over 3 years ago

10.3389/fninf.2020.572068

Rxnat: An Open-Source R Package for XNAT-Based Repositories
Cited by: 0
Author(s): Adrian Gherman, John Muschelli, Brian Caffo, Ciprian M. Crainiceanu
Software Mentions: 13
Published: almost 4 years ago

10.1371/journal.pcbi.1007859

Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease
Cited by: 10
Author(s): Christine Tataru, Maude M. David
Software Mentions: 13
Published: over 4 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: over 3 years ago

10.12688/f1000research.15949.2

The Mega2R package: R tools for accessing and processing genetic data in common formats
Cited by: 0
Author(s): R. Baron, Justin R. Stickel, Daniel E. Weeks
Software Mentions: 12
Published: over 5 years ago

10.1038/s41598-018-20825-z

Mosquito community influences West Nile virus seroprevalence in wild birds: implications for the risk of spillover into human populations
Cited by: 30
Author(s): Josué Martínez‐de la Puente, Martina Ferraguti, Santiago Ruíz, David Roiz, Francisco Rubio Llorente, Elisa Pérez‐Ramírez, Miguel Ángel Jiménez‐Clavero, Ramón C. Soriguer, Jordi Figuerola
Software Mentions: 11
Published: over 6 years ago

10.1002/1878-0261.12134

Tissue glycomics distinguish tumour sites in women with advanced serous adenocarcinoma
Cited by: 21
Author(s): Merrina Anugraham, Francis Jacob, Arun Everest‐Dass, Andreas Schoetzau, Sheri Nixdorf, Neville F. Hacker, Daniel Fink, Viola Heinzelmann‐Schwarz, Nicolle H. Packer
Software Mentions: 11
Published: about 7 years ago

10.1371/journal.pcbi.1006135

beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types
Cited by: 13
Author(s): Aaron T. L. Lun, Hervé Pagès, Mike L. Smith
Software Mentions: 10
Published: over 6 years ago

10.12688/f1000research.11997.1

valr: Reproducible genome interval analysis in R
Cited by: 43
Author(s): Kent Riemondy, Ryan M. Sheridan, Austin E. Gillen, Yinni Yu, Christopher Bennett, Jay R. Hesselberth
Software Mentions: 10
Published: over 7 years ago

10.1371/journal.pone.0191206

Prognostic relevance of elevated pulmonary arterial pressure assessed non-invasively: Analysis in a large patient cohort with invasive measurements in near temporal proximity
Cited by: 3
Author(s): Steffen Greiner, Andreas Jud, Matthias Aurich, Christoph Geisenberger, Lorenz Uhlmann, Thomas Hilbel, Meinhard Kieser, Hugo A. Katus, Derliz Mereles
Software Mentions: 10
Published: over 6 years ago

10.1186/s12859-015-0613-1

tcR: an R package for T cell receptor repertoire advanced data analysis
Cited by: 199
Author(s): Vadim Nazarov, Mikhail V. Pogorelyy, Ekaterina A. Komech, Ivan V. Zvyagin, Dmitriy A. Bolotin, Mikhail Shugay, Dmitriy M. Chudakov, Yuri B. Lebedev, Ilgar Z. Mamedov
Software Mentions: 10
Published: over 9 years ago

10.1080/19336896.2020.1751574

Estimation of amyloid aggregate sizes with semi-denaturing detergent agarose gel electrophoresis and its limitations
Cited by: 10
Author(s): Polina Drozdova, Yury A. Barbitoff, М. В. Белоусов, Rostislav K. Skitchenko, Tatyana Rogoza, Jeremy Y Leclercq, Andrey V. Kajava, Andrew G. Matveenko, Galina A. Zhouravleva, Stanislav A. Bondarev
Software Mentions: 10
Published: almost 5 years ago

10.1371/journal.pcbi.1006369

SILGGM: An extensive R package for efficient statistical inference in large-scale gene networks
Cited by: 35
Author(s): Rong Zhang, Zhao Ren, Wei Chen
Software Mentions: 10
Published: about 6 years ago

10.3389/fcell.2021.718624

Identification of a Novel Prognostic Gene Signature From the Immune Cell Infiltration Landscape of Osteosarcoma
Cited by: 15
Author(s): Lei Fan, Jingtao Ru, Tao Liu, Chi Ma
Software Mentions: 9
Published: about 3 years ago

10.1371/journal.pone.0226694

AlleleProfileR: A versatile tool to identify and profile sequence variants in edited genomes
Cited by: 4
Author(s): Arne A.N. Bruyneel, Alexandre R. Colas, Ioannis Karakikes, Mark Mercola
Software Mentions: 9
Published: almost 5 years ago

10.1186/s12859-017-1538-7

stpm: an R package for stochastic process model
Cited by: 4
Author(s): Ilya Y. Zhbannikov, Konstantin G. Arbeev, Igor Akushevich, Eric Stallard, Anatoliy I. Yashin
Software Mentions: 9
Published: over 7 years ago

10.1186/s12859-020-03669-1

TRIP - T cell receptor/immunoglobulin profiler
Cited by: 11
Author(s): Maria Th. Kotouza, Katerina Gemenetzi, Chrysi Galigalidou, Elisavet Vlachonikola, Nikolaos Pechlivanis, Andreas Agathangelidis, Raphael Sandaltzopoulos, Pericles A. Mitkas, Kostas Stamatopoulos, Anastasia Chatzidimitriou, Fotis Psomopoulos
Software Mentions: 9
Published: about 4 years ago

10.1186/1746-6148-10-71

EpiContactTrace: an R-package for contact tracing during livestock disease outbreaks and for risk-based surveillance
Cited by: 45
Author(s): Maria Nöremark, Stefan Widgrén
Software Mentions: 8
Published: almost 11 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: about 7 years ago

10.1186/s12864-021-07918-2

CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis
Cited by: 10
Author(s): Carlos Alberto Oliveira de Biagi, Ricardo Perecin Nociti, Danielle Barbosa Brotto, Breno Osvaldo Funicheli, Patrícia de Cássia Ruy, João Paulo Bianchi Ximenez, David Livingstone Alves Figueiredo, Wilson A. Silva
Software Mentions: 8
Published: about 3 years ago

10.1534/genetics.118.301595

R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations
Cited by: 295
Author(s): Karl W. Broman, Daniel M. Gatti, Petr Šimeček, Nicholas A. Furlotte, Pjotr Prins, Śaunak Sen, Brian S. Yandell, Gary A. Churchill
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0239623

A non-parametric effect-size measure capturing changes in central tendency and data distribution shape
Cited by: 5
Author(s): Jörn Lötsch, Alfred Ultsch
Software Mentions: 8
Published: about 4 years ago

10.1534/g3.119.400373

isqg: A Binary Framework for<i>in Silico</i>Quantitative Genetics
Cited by: 1
Author(s): Fernando H. Toledo, Paulino Pérez‐Rodríguez, J. Crossa, Juan Burgueño
Software Mentions: 8
Published: about 5 years ago

10.3390/cells8101161

An Efficient and Flexible Method for Deconvoluting Bulk RNA-Seq Data with Single-Cell RNA-Seq Data
Cited by: 15
Author(s): Xifang Sun, Shuang Sun, Sheng Yang
Software Mentions: 8
Published: about 5 years ago

10.1371/journal.pone.0197370

Immunity levels to poliovirus in Lao children and adults before the vaccine-derived poliovirus outbreak: A retrospective study
Cited by: 2
Author(s): Maude Pauly, Antony P. Black, Phonepaseuth Khampanisong, Phonethipsavanh Nouanthong, Judith M. Hübschen, Naphavanh Nanthavong, Kong Sayasinh, Prapan Jutavijittum, Bounthome Samountry, Anonh Xeuatvongsa, Sabine Diedrich, Claude P. Muller
Software Mentions: 8
Published: over 6 years ago

10.1534/g3.115.023739

argyle: An R Package for Analysis of Illumina Genotyping Arrays
Cited by: 34
Author(s): Andrew P. Morgan
Software Mentions: 7
Published: over 8 years ago

10.1371/journal.pone.0174606

News exposure predicts anti-Muslim prejudice
Cited by: 35
Author(s): John H. Shaver, Chris G. Sibley, Danny Osborne, Joseph Bulbulia
Software Mentions: 7
Published: over 7 years ago

10.1186/s12859-017-1914-3

bcROCsurface: an R package for correcting verification bias in estimation of the ROC surface and its volume for continuous diagnostic tests
Cited by: 6
Author(s): Khanh To Duc
Software Mentions: 7
Published: almost 7 years ago

10.1186/1471-2164-15-178

seqCNA: an R package for DNA copy number analysis in cancer using high-throughput sequencing
Cited by: 12
Author(s): David Mósen-Ansorena, Naiara Tellería, Silvia Veganzones, Virginia de la Orden, M.L. Maestro, Ana M. Aransay
Software Mentions: 7
Published: almost 11 years ago

10.1186/s12859-019-2899-x

Efficient estimation of grouped survival models
Cited by: 0
Author(s): Zhiguo Li, Jiaxing Lin, Alexander B. Sibley, Tracy Truong, Katherina C. Chua, Yu Jiang, Janice McCarthy, Deanna L. Kroetz, Andrew S. Allen, Kouros Owzar
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0239864

Hybrid algorithms for generating optimal designs for discriminating multiple nonlinear models under various error distributional assumptions
Cited by: 6
Author(s): Chih-Chia Chen, Ping Yang Chen, Cheng Lin Hsu, Weng Kee Wong
Software Mentions: 7
Published: about 4 years ago

10.1098/rsos.160293

Reflections of the social environment in chimpanzee memory: applying rational analysis beyond humans
Cited by: 5
Author(s): Jeffrey R. Stevens, Julian N. Marewski, Lael J. Schooler, Ian C. Gilby
Software Mentions: 7
Published: about 8 years ago

10.1186/s12859-018-2347-3

DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference
Cited by: 6
Author(s): Luc Villandré, Aurélie Labbe, Bluma G. Brenner, Michel Roger, David A. Stephens
Software Mentions: 7
Published: about 6 years ago

10.1038/s41598-021-96403-7

Exercise interventions can improve muscle strength, endurance, and electrical activity of lumbar extensors in individuals with non-specific low back pain: a systematic review with meta-analysis
Cited by: 3
Author(s): Sacha Clael, Lorrane Freitas Campos, Karina Lisboa Correia, Joana Marcela Sales de Lucena, Paulo Gentil, João Luíz Quagliotti Durigan, Alexandre Lima de Araújo Ribeiro, Wagner Rodrigues Martins
Software Mentions: 7
Published: about 3 years ago

10.1038/srep26454

GBIQ: a non-arbitrary, non-biased method for quantification of fluorescent images
Cited by: 2
Author(s): Youichirou Ninomiya, Wei Zhao, Yumiko Saga
Software Mentions: 6
Published: over 8 years ago

10.1186/s12859-020-03715-y

MCMSeq: Bayesian hierarchical modeling of clustered and repeated measures RNA sequencing experiments
Cited by: 8
Author(s): Brian Vestal, Camille M. Moore, Elizabeth Wynn, Laura Saba, Tasha E. Fingerlin, Katerina Kechris
Software Mentions: 6
Published: about 4 years ago

10.1186/s12859-018-2330-z

outbreaker2: a modular platform for outbreak reconstruction
Cited by: 50
Author(s): Finlay Campbell, Xavier Didelot, Richard G. FitzJohn, Neil Ferguson, Anne Cori, Thibaut Jombart
Software Mentions: 6
Published: about 6 years ago

10.1007/s10928-021-09760-1

Pharmacometric estimation methods for aggregate data, including data simulated from other pharmacometric models
Cited by: 1
Author(s): Pyry A. J. Välitalo
Software Mentions: 6
Published: over 3 years ago

10.1186/s12859-015-0581-5

GENLIB: an R package for the analysis of genealogical data
Cited by: 14
Author(s): Héloïse Gauvin, Jean‐François Lefebvre, Claudia Moreau, Ève-Marie Lavoie, Damian Labuda, Hélène Vézina, Marie-Hélène Roy-Gagnon
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.ppat.1009916

Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data
Cited by: 6
Author(s): Gonché Danesh, Victor Virlogeux, Christophe Ramière, Caroline Charre, Laurent Cotte, Samuel Alizon
Software Mentions: 6
Published: about 3 years ago

10.1186/s13059-019-1743-y

CONFINED: distinguishing biological from technical sources of variation by leveraging multiple methylation datasets
Cited by: 6
Author(s): Michael Thompson, Zeyuan Johnson Chen, Elior Rahmani, Eran Halperin
Software Mentions: 6
Published: about 5 years ago

10.1186/s12936-017-2130-3

Towards malaria elimination in Savannakhet, Lao PDR: mathematical modelling driven strategy design
Cited by: 18
Author(s): Sai Thein Than Tun, Lorenz von Seidlein, Tiengkham Pongvongsa, Mayfong Mayxay, Sompob Saralamba, Shwe Sin Kyaw, Phetsavanh Chanthavilay, O. Celhay, Tran Dang Nguyen, Thu Nguyen-Anh Tran, Daniel M. Parker, Maciej F. Boni, Arjen M. Dondorp, Lisa J. White
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pcbi.1005694

PCSF: An R-package for network-based interpretation of high-throughput data
Cited by: 34
Author(s): Murodzhon Akhmedov, Amanda J. Kedaigle, Renan Escalante Chong, Roberto Montemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee
Software Mentions: 6
Published: about 7 years ago

10.7717/peerj-cs.243

HACSim: an R package to estimate intraspecific sample sizes for genetic diversity assessment using haplotype accumulation curves
Cited by: 15
Author(s): Jarrett D. Phillips, Steven H. French, Robert Hanner, Daniel Gillis
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.21778

Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate
Cited by: 36
Author(s): Malene Juul, Johanna Bertl, Qianyun Guo, Morten Muhlig Nielsen, Michał P. Świtnicki, Henrik Hornshøj, Tobias Madsen, Asger Hobolth, Jakob Skou Pedersen
Software Mentions: 5
Published: over 7 years ago

10.1093/g3journal/jkaa017

AlphaSimR: an R package for breeding program simulations
Cited by: 88
Author(s): R. Chris Gaynor, Gregor Gorjanc, John M. Hickey
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13059-014-0527-7

The importance of study design for detecting differentially abundant features in high-throughput experiments
Cited by: 12
Author(s): Huaien Luo, Juntao Li, Burton Kuan Hui Chia, Paul Robson, Niranjan Nagarajan
Software Mentions: 5
Published: almost 10 years ago

10.1186/s12866-020-01845-0

Impacts of a novel defensive symbiosis on the nematode host microbiome
Cited by: 7
Author(s): Dylan Dahan, Gail Preston, Jordan E. Sealey, Kayla C. King
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.68699

Multi-syndrome, multi-gene risk modeling for individuals with a family history of cancer with the novel R package PanelPRO
Cited by: 9
Author(s): Gavin Lee, Jane W. Liang, Qing Zhang, Theodore Huang, Christine Choirat, Giovanni Parmigani, Danielle Braun
Software Mentions: 5
Published: about 3 years ago

10.1002/ece3.4850

Efficient Bayesian analysis of occupancy models with logit link functions
Cited by: 15
Author(s): Allan Clark, Res Altwegg
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pcbi.1007663

RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method
Cited by: 36
Author(s): Kosuke Hamazaki, Hiroyoshi Iwata
Software Mentions: 5
Published: over 4 years ago

10.1186/1471-2105-15-172

hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups
Cited by: 31
Author(s): Mohammad Ferdosi, Brian Kinghorn, J. H. J. van der Werf, Seung H. Lee, Cedric Gondro
Software Mentions: 5
Published: over 10 years ago

10.1007/s00180-021-01102-6

Direct statistical inference for finite Markov jump processes via the matrix exponential
Cited by: 5
Author(s): Chris Sherlock
Software Mentions: 5
Published: over 3 years ago

10.1038/srep09066

Hardy-Weinberg equilibrium revisited for inferences on genotypes featuring allele and copy-number variations
Cited by: 3
Author(s): Andreas Recke, Klaus-Günther Recke, Saleh M. Ibrahim, Steffen Möller, Reinhard Vonthein
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0163711

hemaClass.org: Online One-By-One Microarray Normalization and Classification of Hematological Cancers for Precision Medicine
Cited by: 7
Author(s): Steffen Falgreen, Anders Ellern Bilgrau, Rasmus Froberg Brøndum, Lasse Hjort Jakobsen, Jonas Have, Kasper Lindblad Nielsen, Tarec Christoffer El‐Galaly, Julie Støve Bødker, Alexander Schmitz, Ken H. Young, Hans Erik Johnsen, Karen Dybkær, Martin Bøgsted
Software Mentions: 5
Published: about 8 years ago

10.1186/s12859-020-03862-2

Mixed logistic regression in genome-wide association studies
Cited by: 2
Author(s): Jacqueline Milet, David Courtin, André Garcia, Hervé Perdry
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12859-021-03981-4

cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large, bacterial whole genome sequencing datasets
Cited by: 10
Author(s): Ryan Crawford, Evan S. Snitkin
Software Mentions: 5
Published: over 3 years ago

10.1186/s12859-020-03725-w

Seagull: lasso, group lasso and sparse-group lasso regularization for linear regression models via proximal gradient descent
Cited by: 15
Author(s): Jan Klosa, Noah Simon, Pål O. Westermark, Volkmar Liebscher, Dörte Wittenburg
Software Mentions: 5
Published: about 4 years ago

10.1186/s12859-015-0597-x

ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles
Cited by: 30
Author(s): Catalina Anghel, Gerald Quon, Syed Haider, Francis Nguyen, Amit G. Deshwar, Quaid Morris, Paul C. Boutros
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0238285

Increased risk of adverse events in non-cancer patients with chronic and high-dose opioid use—A health insurance claims analysis
Cited by: 6
Author(s): Jakob M Burgstaller, Ulrike Held, Andri Signorell, Eva Blozik, Johann Steurer, Maria M. Wertli
Software Mentions: 5
Published: about 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/s12859-019-2869-3

fastJT: An R package for robust and efficient feature selection for machine learning and genome-wide association studies
Cited by: 1
Author(s): Jiaxing Lin, Alexander B. Sibley, Ivo Shterev, Andrew B. Nixon, Federico Innocenti, Cliburn Chan, Kouros Owzar
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-017-1554-7

SFREEMAP - A simulation-free tool for stochastic mapping
Cited by: 3
Author(s): Diego Pasqualin, Marcos S. Barbeitos, Fabiano Silva
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2105-14-204

Deconvolution of gene expression from cell populations across the C. eleganslineage
Cited by: 2
Author(s): Joshua T. Burdick, John I. Murray
Software Mentions: 4
Published: over 11 years ago

10.1128/AEM.02343-19

Reintroducing mothur: 10 Years Later
Cited by: 132
Author(s): Patrick D. Schloss
Software Mentions: 4
Published: over 4 years ago

10.1186/s12913-017-2086-6

Changes over time in prescription practices of pain medications in Switzerland between 2006 and 2013: an analysis of insurance claims
Cited by: 34
Author(s): Maria M. Wertli, Oliver Reich, Andri Signorell, Jakob M Burgstaller, Johann Steurer, Ulrike Held
Software Mentions: 4
Published: over 7 years ago

10.1186/s12936-021-03726-x

The assembly effect: the connectedness between populations is a double‐edged sword for public health interventions
Cited by: 2
Author(s): Sai Thein Than Tun, Daniel M. Parker, Ricardo Águas, Lisa J. White
Software Mentions: 4
Published: over 3 years ago

10.7717/peerj.1487

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units
Cited by: 224
Author(s): Sarah L. Westcott, Patrick D. Schloss
Software Mentions: 4
Published: almost 9 years ago

10.1002/pld3.53

Farm<scp>CPU</scp>pp: Efficient large‐scale genomewide association studies
Cited by: 22
Author(s): Aaron Kusmec, Patrick S. Schnable
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1004755

FastGGM: An Efficient Algorithm for the Inference of Gaussian Graphical Model in Biological Networks
Cited by: 55
Author(s): Ting Wang, Zhao Ren, Ying Ding, Zhou Fang, Zhe Sun, Matthew L. MacDonald, Robert A. Sweet, Jieru Wang, Wei Chen
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pcbi.1007972

Heterogeneous, delayed-onset killing by multiple-hitting T cells: Stochastic simulations to assess methods for analysis of imaging data
Cited by: 7
Author(s): Richard J. Beck, Dario I. Bijker, Joost B. Beltman
Software Mentions: 4
Published: about 4 years ago

10.1002/ece3.6691

Leaf shape in <i>Populus tremula</i> is a complex, omnigenic trait
Cited by: 17
Author(s): Niklas Mähler, Bastian Schiffthaler, Kathryn M. Robinson, Barbara K Terebieniec, Matej Vučak, Chanaka Mannapperuma, Mark E.S. Bailey, Stefan Jansson, Torgeir R. Hvidsten, Nathaniel R. Street
Software Mentions: 4
Published: almost 4 years ago

10.3389/fgene.2021.655287

TrainSel: An R Package for Selection of Training Populations
Cited by: 13
Author(s): Deniz Akdemir, Simon Rio, Julio Isidro Sanchéz
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2021.705381

Antibody Repertoire Analysis of Tumor-Infiltrating B Cells Reveals Distinct Signatures and Distributions Across Tissues
Cited by: 7
Author(s): Ligal Aizik, Yael Dror, David Taussig, Adi Barzel, Yaron Carmi, Yariv Wine
Software Mentions: 4
Published: about 3 years ago

10.3390/genes11060634

metaRE R Package for Meta-Analysis of Transcriptome Data to Identify the cis-Regulatory Code behind the Transcriptional Reprogramming
Cited by: 7
Author(s): Daria D. Novikova, Pavel Cherenkov, Yana Sizentsova, В. В. Миронова
Software Mentions: 4
Published: over 4 years ago

10.1186/s13073-019-0643-9

Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time
Cited by: 8
Author(s): Paul Little, Danyu Lin, Wei Sun
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-017-12401-8

Similarity-Based Segmentation of Multi-Dimensional Signals
Cited by: 14
Author(s): Rainer Machné, Douglas B. Murray, Peter F. Stadler
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-017-16520-0

propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis
Cited by: 130
Author(s): Thomas P. Quinn, Mark F. Richardson, David Lovell, Tamsyn M. Crowley
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-018-38348-y

Crossword: A data-driven simulation language for the design of genetic-mapping experiments and breeding strategies
Cited by: 0
Author(s): Walid Korani, Justin N. Vaughn
Software Mentions: 4
Published: over 5 years ago

10.18632/oncotarget.6679

Computational selection of antibody-drug conjugate targets for breast cancer
Cited by: 13
Author(s): François Fauteux, Jonathan D. Hill, María Jaramillo, Youlian Pan, Sieu Phan, Fazel Famili, Maureen D. O'Connor‐McCourt
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12711-019-0456-8

Removal of alleles by genome editing (RAGE) against deleterious load
Cited by: 45
Author(s): Martin Johnsson, R. Chris Gaynor, Janez Jenko, Gregor Gorjanc, Dirk-Jan de Koning, John M. Hickey
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pcbi.1004978

Computationally Efficient Implementation of a Novel Algorithm for the General Unified Threshold Model of Survival (GUTS)
Cited by: 8
Author(s): Carlo Albert, Sören Vogel, Roman Ashauer
Software Mentions: 3
Published: over 8 years ago

10.1093/bioinformatics/btw705

KODAMA: an R package for knowledge discovery and data mining
Cited by: 28
Author(s): Stefano Cacciatore, Leonardo Tenori, Claudio Luchinat, Phillip R. Bennett, David A. MacIntyre
Software Mentions: 3
Published: almost 8 years ago

10.7717/peerj-cs.600

Clustering assessment in weighted networks
Cited by: 2
Author(s): Argimiro Arratia, Martí Renedo Mirambell
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.48401

Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence
Cited by: 83
Author(s): Cara E. Brook, Mike Boots, Kartik Chandran, Andrew Dobson, Christian Drosten, Andrea L. Graham, Bryan T. Grenfell, Marcel A. Müller, Melinda Ng, Lin‐Fa Wang, Anieke van Leeuwen
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-020-02125-w

Primo: integration of multiple GWAS and omics QTL summary statistics for elucidation of molecular mechanisms of trait-associated SNPs and detection of pleiotropy in complex traits
Cited by: 24
Author(s): Kevin J. Gleason, Fan Yang, Brandon L. Pierce, Xin He, Lin S. Chen
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pcbi.1004382

Flexible Modeling of Epidemics with an Empirical Bayes Framework
Cited by: 102
Author(s): Logan Brooks, David Farrow, Sangwon Hyun, Ryan J. Tibshirani, Roni Rosenfeld
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0101205

Movement-Based Estimation and Visualization of Space Use in 3D for Wildlife Ecology and Conservation
Cited by: 46
Author(s): Jeff A. Tracey, James K. Sheppard, Jun Zhu, Fuwen Wei, Ronald R. Swaisgood, Robert N. Fisher
Software Mentions: 3
Published: over 10 years ago

Projects: cran: Rcpp

Papers Mentioning Rcpp 152