cran: devtools | Projects | Ecosyste.ms: Papers

10.12688/f1000research.8694.1

IncucyteDRC: An R package for the dose response analysis of live cell imaging data
Cited by: 8
Author(s): Phil Chapman, Dominic I. James, Amanda J. Watson, Gemma Hopkins, Ian D. Waddell, Donald Ogilvie
Software Mentions: 5
Published: over 8 years ago

10.3389/fcell.2020.560766

Transcriptome Reveals Multi Pigmentation Genes Affecting Dorsoventral Pattern in Avian Body
Cited by: 6
Author(s): Xi Yang, Hehe Liu, Li Liang, Qian Xu, Yisi Liu, Lei Wang, Shengchao Ma, Jianmei Wang, Lili Bai, Rongping Zhang, Chunchun Han
Software Mentions: 5
Published: about 4 years ago

10.3389/fcimb.2020.00072

Mucosal Microbiome Profiles Polygenic Irritable Bowel Syndrome in Mestizo Individuals
Cited by: 4
Author(s): René Arredondo‐Hernández, Max Schmulson, Patricia Orduña, Gamaliel López-Leal, Ángel-Mario Zárate, Gerardo J. Alanis-Funes, Luis David Alcaraz, Rubí Santiago-Cruz, Miguel A. Cevallos, Antonio Villa, Samuel Ponce-de-León Rosales, Yolanda López‐Vidal, Consorcio Mexicano para el Estudio del Microbioma Humano
Software Mentions: 5
Published: over 4 years ago

10.3389/fimmu.2021.614246

Reduced Placental Transfer of Antibodies Against a Wide Range of Microbial and Vaccine Antigens in HIV-Infected Women in Mozambique
Cited by: 10
Author(s): Selena Alonso, Marta Vidal, Gemma Ruiz‐Olalla, Raquel González, Maria Nélia Manaca, Chenjerai Jairoce, Miquel Vázquez-Santiago, Reyes Balcells, Anifa Valá, Maria Rosario, Pau Cisteró, Laura Fuente-Soro, Marta Cova, Evelina Angov, Arsénio Nhacolo, Esperança Sevene, John J. Aponte, Eusébio Macete, Ruth Aguilar, Alfredo Mayor, Clara Menéndez, Carlota Dobaño, Gemma Moncunill
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2018.00785

SplinectomeR Enables Group Comparisons in Longitudinal Microbiome Studies
Cited by: 44
Author(s): Robin R. Shields-Cutler, Gabe A. Al-Ghalith, Moran Yassour, Dan Knights
Software Mentions: 5
Published: over 6 years ago

10.3389/fpls.2020.511768

R/UAStools::plotshpcreate: Create Multi-Polygon Shapefiles for Extraction of Research Plot Scale Agriculture Remote Sensing Data
Cited by: 14
Author(s): Steven L. Anderson, Seth C. Murray
Software Mentions: 5
Published: about 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

10.2196/22179

Online Patient Recruitment in Clinical Trials: Systematic Review and Meta-Analysis
Cited by: 53
Author(s): Mette Brøgger-Mikkelsen, Zarqa Ali, John R. Zibert, Anette Andersen, Simon Francis Thomsen
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0189419

Caliver: An R package for CALIbration and VERification of forest fire gridded model outputs
Cited by: 9
Author(s): Claudia Vitolo, Francesca Di Giuseppe, Mirko D’Andrea
Software Mentions: 4
Published: almost 7 years ago

10.12688/f1000research.9742.2

whoishRisk – an R package to calculate WHO/ISH cardiovascular risk scores for all epidemiological subregions of the world
Cited by: 14
Author(s): Dylan Collins, Joseph Lee, Niklas Bobrovitz, Constantinos Koshiaris, Alison Ward, Carl Heneghan
Software Mentions: 4
Published: over 7 years ago

10.3389/fpsyg.2020.00169

A Bayesian Approach to the Analysis of Local Average Treatment Effect for Missing and Non-normal Data in Causal Modeling: A Tutorial With the ALMOND Package in R
Cited by: 4
Author(s): Dingjing Shi, Xin Tong, Marvin C. Meyer
Software Mentions: 4
Published: over 4 years ago

10.3389/fpsyg.2015.01782

Thinking Outside the Box: Developing Dynamic Data Visualizations for Psychology with Shiny
Cited by: 31
Author(s): David Ellis, Hannah Lena Merdian
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0222016

Impact of care provider network characteristics on patient outcomes: Usage of social network analysis and a multi-scale community detection
Cited by: 13
Author(s): Mina Ostovari, Denny Yu
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0179886

Morphological and genetic diversity of camu-camu [Myrciaria dubia (Kunth) McVaugh] in the Peruvian Amazon
Cited by: 10
Author(s): Jan Šmíd, Marie Kalousová, Bohumil Mandák, Jakub Houška, Anna Chládová, Mario Pinedo, Bohdan Lojka
Software Mentions: 4
Published: over 7 years ago

10.3390/ani9060372

Food Preferences in Cats: Effect of Dietary Composition and Intrinsic Variables on Diet Selection
Cited by: 6
Author(s): Raúl Alegría-Morán, Sergio A. Guzmán-Pino, Juan Ignacio Egaña, Valeria Sotomayor, Jaime Figueroa
Software Mentions: 4
Published: over 5 years ago

10.1111/jcmm.14045

Inhibition of miR-148a-3p resists hepatocellular carcinoma progress of hepatitis C virus infection through suppressing<i>c-Jun</i>and MAPK pathway
Cited by: 27
Author(s): Yibin Deng, Jianchu Wang, Meijin Huang, Guidan Xu, Wujun Wei, Houji Qin
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pcbi.1007770

A framework for integrating directed and undirected annotations to build explanatory models of cis-eQTL data
Cited by: 2
Author(s): David Lamparter, Rajat Bhatnagar, Katja Hebestreit, T. Grant Belgard, Alice Zhang, Victor Hanson-Smith
Software Mentions: 4
Published: over 4 years ago

10.3390/microorganisms9051038

Microbial Hotspots in Lithic Microhabitats Inferred from DNA Fractionation and Metagenomics in the Atacama Desert
Cited by: 15
Author(s): Dirk Schulze‐Makuch, Daniel Lipus, Felix L. Arens, Mickaël Baqué, Till L. V. Bornemann, Jean Pierre Paul de Vera, Markus Flury, Jan Frösler, Jacob Heinz, Yunha Hwang, Samuel P. Kounaves, Kai Mangelsdorf, Rainer U. Meckenstock, Mark Pannekens, Alexander J. Probst, Johan S. Sáenz, Janosch Schirmack, Michael Schloter, Philippe Schmitt‐Kopplin, Bernd Uwe Schneider, Jenny Uhl, Gisle Vestergaard, Bernardita Valenzuela, Pedro Zamorano, Dirk Wagner
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-017-17143-1

Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes
Cited by: 16
Author(s): Jigar Desai, Ryan C. Sartor, Lovely Mae F Lawas, S. V. Krishna Jagadish, Colleen J. Doherty
Software Mentions: 4
Published: almost 7 years ago

10.1099/mgen.0.000245

HomoplasyFinder: a simple tool to identify homoplasies on a phylogeny
Cited by: 48
Author(s): Joseph Crispell, Daniel Balaz, Stephen V. Gordon
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12870-020-02581-3

Activities of leaf and spike carbohydrate-metabolic and antioxidant enzymes are linked with yield performance in three spring wheat genotypes grown under well-watered and drought conditions
Cited by: 29
Author(s): Sajid Shokat, Dominik K. Großkinsky, Thomas Roitsch, Fulai Liu
Software Mentions: 4
Published: about 4 years ago

10.1186/s13075-020-02343-4

Single-cell transcriptome conservation in a comparative analysis of fresh and cryopreserved human skin tissue: pilot in localized scleroderma
Cited by: 17
Author(s): Emily Mirizio, Tracy Tabib, Xinjun Wang, Wei Chen, Christopher Liu, Robert Lafyatis, Heidi Jacobe, Kathryn S. Torok
Software Mentions: 4
Published: almost 4 years ago

10.3390/ani9050219

Food Preferences in Dogs: Effect of Dietary Composition and Intrinsic Variables on Diet Selection
Cited by: 16
Author(s): Raúl Alegría-Morán, Sergio A. Guzmán-Pino, Juan Ignacio Egaña, C. Gascón Muñoz, Jaime Figueroa
Software Mentions: 4
Published: over 5 years ago

10.3390/ani11071950

Investigating the Effects of a Phytobiotics-Based Product on the Fecal Bacterial Microbiome of Weaned Pigs
Cited by: 8
Author(s): Anlly Fresno Rueda, Ryan S Samuel, Benoit St‐Pierre
Software Mentions: 4
Published: over 3 years ago

10.3389/fnmol.2019.00293

Identification of lncRNAs Associated With Neuroblastoma in Cross-Sectional Databases: Potential Biomarkers
Cited by: 13
Author(s): Bharat Prajapati, Mena Fatma, Mahar Fatima, Tipu Khan, Subrata Sinha, Prahlad K. Seth
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pcbi.1007132

Information-theoretic analysis of multivariate single-cell signaling responses
Cited by: 34
Author(s): Tomasz Jetka, Karol Nienałtowski, Tomasz Winarski, Sławomir Błoński, Michał Komorowski
Software Mentions: 3
Published: about 5 years ago

10.1007/s00253-019-09701-6

Uncovering carbohydrate metabolism through a genotype-phenotype association study of 56 lactic acid bacteria genomes
Cited by: 52
Author(s): G. Buron-Moles, Anna Chailyan, Igor Dolejš, Jochen Förster, Marta Hanna Mikš
Software Mentions: 3
Published: over 5 years ago

10.1093/braincomms/fcab105

Use of high-content imaging to quantify transduction of AAV-PHP viruses in the brain following systemic delivery
Cited by: 6
Author(s): Edward J. Smith, Pamela Farshim, Rachel Flomen, Samuel T. Jones, Sean J McAteer, Benjamin E. Deverman, Viviana Gradinaru, Gillian P. Bates
Software Mentions: 3
Published: over 3 years ago

10.1242/dmm.048977

High-dimensional immunotyping of tumors grown in obese and non-obese mice
Cited by: 8
Author(s): Cara E. Wogsland, Hilde Lien, Lykke Pedersen, Pahul Hanjra, Sturla Magnus Grøndal, Rolf A. Brekken, James B. Lorens, Nils Halberg
Software Mentions: 3
Published: over 3 years ago

10.3389/fpsyg.2021.628728

Controlling Video Stimuli in Sign Language and Gesture Research: The OpenPoseR Package for Analyzing OpenPose Motion-Tracking Data in R
Cited by: 5
Author(s): Patrick C. Trettenbrein, Emiliano Zaccarella
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-86626-z

Molecular diversity of Mycobacterium tuberculosis complex in Sikkim, India and prediction of dominant spoligotypes using artificial intelligence
Cited by: 11
Author(s): Kangjam Rekha Devi, Jagat Pradhan, Rinchenla Bhutia, Peggy Dadul, Achyut Sarkar, Nitumoni Gohain, Kanwar Narain
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0192520

Correction: Gbm.auto: A software tool to simplify spatial modelling and Marine Protected Area planning
Cited by: 0
Author(s): Simon Dedman, Rick Officer, Maurice Clarke, David G. Reid, Deirdre Brophy
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-021-96513-2

Theory of mind affects the interpretation of another person's focus of attention
Cited by: 0
Author(s): Jessica Dawson, Alan Kingstone, Tom Foulsham
Software Mentions: 3
Published: about 3 years ago

10.12688/f1000research.27214.2

iCAT: diagnostic assessment tool of immunological history using high-throughput T-cell receptor sequencing
Cited by: 2
Author(s): Ahmad Rajeh, Kyle J. Wolf, Courtney Schiebout, Nabeel Sait, Tim Kosfeld, Richard J. DiPaolo, Tae-Hyuk Ahn
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0243841

An R Package for Computing Canadian Assessment of Physical Literacy (CAPL) scores and interpretations from raw data
Cited by: 2
Author(s): Joel D. Barnes, Michelle D. Guerrero
Software Mentions: 3
Published: over 3 years ago

10.12688/gatesopenres.13211.1

Fpemlocal: Estimating family planning indicators in R for a single population of interest
Cited by: 2
Author(s): Gregory Guranich, Niamh Cahill, Leontine Alkema
Software Mentions: 3
Published: over 3 years ago

10.3390/genes12040463

Evidence Supporting the Regulatory Relationships through a Paracrine Pathway between the Sternum and Pectoral Muscles in Ducks
Cited by: 0
Author(s): Yanying Li, Hehe Liu, Lei Wang, Xi Yang, Jiwen Wang, Rongping Zhang, Liang Li, Lili Bai, Ahsan Mustafa
Software Mentions: 3
Published: over 3 years ago

10.1186/s40621-018-0149-8

Open-access programs for injury categorization using ICD-9 or ICD-10
Cited by: 74
Author(s): David E. Clark, Adam Black, David H. Skavdahl, Lee D. Hallagan
Software Mentions: 3
Published: over 6 years ago

10.3390/ijerph15071464

Role of Sediments in Insecticide Runoff from Urban Surfaces: Analysis and Modeling
Cited by: 26
Author(s): Angela Gorgoglione, Fabián A. Bombardelli, Bruno J. L. Pitton, Lorence R. Oki, Darren Haver, Thomas M. Young
Software Mentions: 3
Published: about 6 years ago

10.1038/s41597-020-00702-z

LCVP, The Leipzig catalogue of vascular plants, a new taxonomic reference list for all known vascular plants
Cited by: 47
Author(s): Martin Freiberg, Marten Winter, Alessandro Gentile, Alexander Zizka, Alexandra N. Muellner‐Riehl, Alexandra Weigelt, Christian Wirth
Software Mentions: 3
Published: almost 4 years ago

10.7717/peerj.10412

Bacterial exposure leads to variable mortality but not a measurable increase in surface antimicrobials across ant species
Cited by: 0
Author(s): Omar Halawani, Robert R. Dunn, Amy M. Grunden, Adrian A. Smith
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12859-016-1392-z

Finding an appropriate equation to measure similarity between binary vectors: case studies on Indonesian and Japanese herbal medicines
Cited by: 13
Author(s): Sony Hartono Wijaya, Farit Mochamad Afendi, Irmanida Batubara, Latifah Kosim Darusman, Md. Altaf-Ul-Amin, Shigehiko Kanaya
Software Mentions: 3
Published: almost 8 years ago

10.3389/fcimb.2019.00217

Sequential Changes in the Host Gut Microbiota During Infection With the Intestinal Parasitic Nematode Strongyloides venezuelensis
Cited by: 25
Author(s): Tanzila Afrin, Kazunori Murase, Asuka Kounosu, Vicky L. Hunt, Mark W. Bligh, Y. Maeda, Akinori Hino, Haruhiko Maruyama, Isheng Jason Tsai, Taisei Kikuchi
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-40976-x

High-throughput epitope profiling of antibodies in the plasma of Alzheimer’s disease patients using random peptide microarrays
Cited by: 11
Author(s): Kyu-Young Sim, Sangheon Park, Kyu Yeong Choi, Jung Eun Park, Jung Sup Lee, Byeong C. Kim, Jeonghwan Gwak, Woo Keun Song, Kun Ho Lee, Sung‐Gyoo Park
Software Mentions: 3
Published: over 5 years ago

10.1099/mgen.0.000469

Hogwash: three methods for genome-wide association studies in bacteria
Cited by: 11
Author(s): Katie Saund, Evan S. Snitkin
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-017-3990-1

Assisted clustering of gene expression data using ANCut
Cited by: 10
Author(s): Sebastian J. Teran Hidalgo, Mengyun Wu, Shuangge Ma
Software Mentions: 2
Published: about 7 years ago

10.3389/fpls.2021.704239

A Large Root Phenome Dataset Wide-Opened the Potential for Underground Breeding in Soybean
Cited by: 6
Author(s): Ki-Seung Kim, Se‐Hun Kim, Jae‐Young Kim, Pooja Tripathi, Jeong‐Dong Lee, Yong Suk Chung, Yoon-Ha Kim
Software Mentions: 2
Published: about 3 years ago

10.1186/s12284-016-0119-0

Population Dynamics Among six Major Groups of the Oryza rufipogon Species Complex, Wild Relative of Cultivated Asian Rice
Cited by: 43
Author(s): Hyun Jung Kim, Janelle Jung, Namrata Singh, Anthony J. Greenberg, Jeff J. Doyle, Wricha Tyagi, Jong‐Wook Chung, Jennifer Kimball, Ruaraidh Sackville Hamilton, Susan R. McCouch
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pcbi.1004796

BIITE: A Tool to Determine HLA Class II Epitopes from T Cell ELISpot Data
Cited by: 4
Author(s): Lies Boelen, Patrick K. O’Neill, Kathryn Quigley, Catherine J. Reynolds, Bernard Maillère, John H. Robinson, Ganjana Lertmemongkolchai, Daniel M. Altmann, Rosemary J. Boyton, Becca Asquith
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj-cs.544

Connecting virtual reality and ecology: a new tool to run seamless immersive experiments in R
Cited by: 1
Author(s): Julie Vercelloni, Jon Peppinck, Edgar Santos–Fernández, Miles McBain, Grace Heron, Tanya Dodgen, Erin E. Peterson, Kerrie Mengersen
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-020-63471-0

Long-term high-grain diet alters ruminal pH, fermentation, and epithelial transcriptomes, leading to restored mitochondrial oxidative phosphorylation in Japanese Black cattle
Cited by: 5
Author(s): Toru Ogata, Hiroki Makino, Naoki Ishizuka, Eiji Iwamoto, Masaki Terabe, Keiichiro Kizaki, Yo-Han Kim, Shigeru Satō
Software Mentions: 2
Published: over 4 years ago

10.1038/s41597-021-01049-9

The Avian Diet Database as a source of quantitative information on bird diets
Cited by: 2
Author(s): Allen H. Hurlbert, Aaron M. Olsen, Melissa M. Sawyer, Patrick M. Winner
Software Mentions: 2
Published: about 3 years ago

10.3390/diagnostics3010192

Analysis of Predictive Values Based on Individual Risk Factors in Multi-Modality Trials
Cited by: 7
Author(s): Katharina Lange, Edgar Brunner
Software Mentions: 2
Published: over 11 years ago

10.3897/BDJ.8.e49943

SquamataBase: a natural history database and R package for comparative biology of snake feeding habits
Cited by: 18
Author(s): Michael C. Gründler
Software Mentions: 2
Published: over 4 years ago

10.2196/16204

PediTools Electronic Growth Chart Calculators: Applications in Clinical Care, Research, and Quality Improvement
Cited by: 162
Author(s): Joseph H. Chou, Sergei Roumiantsev, Rachana Singh
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-018-23111-0

Same habitat types but different use: evidence of context-dependent habitat selection in roe deer across populations
Cited by: 14
Author(s): William Gaudry, Jean‐Michel Gaillard, Sonia Saı̈d, Christophe Bonenfant, Atle Mysterud, Nicolas Morellet, Maryline Pellerin, Christophe Clément
Software Mentions: 2
Published: over 6 years ago

10.1093/bioinformatics/btaa181

How to get your goat: automated identification of species from MALDI-ToF spectra
Cited by: 10
Author(s): Simon Hickinbotham, Sarah Fiddyment, Timothy L. Stinson, Matthew J. Collins
Software Mentions: 2
Published: over 4 years ago

Projects: cran: devtools

Papers Mentioning devtools 157