cran: caTools | Projects | Ecosyste.ms: Papers

10.12688/f1000research.17824.2

Enhancing gene set enrichment using networks
Cited by: 2
Author(s): Michael Prummer
Software Mentions: 51
Published: over 5 years ago

10.3390/cancers13092163

Spatial Distribution of Private Gene Mutations in Clear Cell Renal Cell Carcinoma
Cited by: 10
Author(s): Ariane L. Moore, Aashil A. Batavia, Jack Kuipers, Jochen Singer, Elodie Burcklen, Peter Schraml, Christian Beisel, Holger Moch, Niko Beerenwinkel
Software Mentions: 20
Published: over 3 years ago

10.1186/s12888-020-02645-6

Depression, anxiety, and burnout among medical students and residents of a medical school in Nepal: a cross-sectional study
Cited by: 66
Author(s): Nishan Babu Pokhrel, Ramesh Khadayat, P Tulachan
Software Mentions: 14
Published: over 4 years ago

10.1371/journal.pone.0207491

Feature selection and prediction of treatment failure in tuberculosis
Cited by: 30
Author(s): Christopher Martin Sauer, David Sasson, Kenneth E. Paik, Ned McCague, Leo Anthony Celi, Iván Sánchez Fernández, Ben Illigens
Software Mentions: 12
Published: about 6 years ago

10.1186/s12864-017-3819-y

RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples
Cited by: 67
Author(s): Petr V. Nazarov, Arnaud Muller, Tony Kaoma, Nathalie Nicot, Cristina Máximo, Philippe Birembaut, Nhan L. Tran, Gunnar Dittmar, Laurent Vallar
Software Mentions: 11
Published: over 7 years ago

10.3390/jcm8091298

Comparison of Machine Learning Techniques for Prediction of Hospitalization in Heart Failure Patients
Cited by: 32
Author(s): Giulia Lorenzoni, Stefano Santo Sabato, Corrado Lanera, Daniele Bottigliengo, Clara Minto, Honoria Ocagli, Paola De Paolis, Darío Gregori, Sabino Iliceto, Franco Pisanò
Software Mentions: 10
Published: over 5 years ago

10.1186/s13104-016-1945-2

Feature selection and validated predictive performance in the domain of Legionella pneumophila: a comparative study
Cited by: 9
Author(s): Tjeerd van der Ploeg, Ewout W. Steyerberg
Software Mentions: 9
Published: almost 9 years ago

10.1371/journal.pone.0247330

Prediction of femoral osteoporosis using machine-learning analysis with radiomics features and abdomen-pelvic CT: A retrospective single center preliminary study
Cited by: 18
Author(s): Hyun Lim, Hong Il Ha, Sun-Young Park, Junhee Han
Software Mentions: 9
Published: almost 4 years ago

10.3390/microorganisms8040485

Characterization of the Duodenal Mucosal Microbiome in Obese Adult Subjects by 16S rRNA Sequencing
Cited by: 33
Author(s): Carmela Nardelli, Ilaria Granata, Valeria D’Argenio, Salvatore Tramontano, Debora Compare, Mario Rosario Guarracino, Gerardo Nardone, Vincenzo Pilone, Lucia Sacchetti
Software Mentions: 8
Published: almost 5 years ago

10.1186/1471-2105-12-467

Empirical comparison of cross-platform normalization methods for gene expression data
Cited by: 88
Author(s): Jason R. Rudy, Faramarz Valafar
Software Mentions: 8
Published: about 13 years ago

10.1186/s13148-018-0453-8

Peripheral blood epi-signature of Claes-Jensen syndrome enables sensitive and specific identification of patients and healthy carriers with pathogenic mutations in KDM5C
Cited by: 55
Author(s): Laila C. Schenkel, Erfan Aref‐Eshghi, Cindy Skinner, Peter Ainsworth, Hanxin Lin, Guillaume Paré, David I. Rodenhiser, Charles E. Schwartz, Bekim Sadiković
Software Mentions: 7
Published: almost 7 years ago

10.3389/fgene.2019.01372

4See: A Flexible Browser to Explore 4C Data
Cited by: 12
Author(s): Yousra Ben Zouari, Angeliki Platania, Anne Molitor, Tom Sexton
Software Mentions: 7
Published: almost 5 years ago

10.3390/metabo11050326

Exploration of Blood Lipoprotein and Lipid Fraction Profiles in Healthy Subjects through Integrated Univariate, Multivariate, and Network Analysis Reveals Association of Lipase Activity and Cholesterol Esterification with Sex and Age
Cited by: 4
Author(s): Yasmijn Balder, Alessia Vignoli, Leonardo Tenori, Claudio Luchinat, Edoardo Saccenti
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0143309

Spatial Patterns in Water Quality Changes during Dredging in Tropical Environments
Cited by: 48
Author(s): Rebecca Fisher, Clair Stark, Peter V. Ridd, Ross Jones
Software Mentions: 6
Published: about 9 years ago

10.2196/14330

Use of Machine Learning Techniques for Case-Detection of Varicella Zoster Using Routinely Collected Textual Ambulatory Records: Pilot Observational Study
Cited by: 5
Author(s): Corrado Lanera, Paola Berchialla, Ileana Baldi, Giulia Lorenzoni, Lara Tramontan, Antonio Scamarcia, Luigi Cantarutti, Carlo Giaquinto, Darío Gregori
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0255838

Optimal distribution-preserving downsampling of large biomedical data sets (opdisDownsampling)
Cited by: 9
Author(s): Jörn Lötsch, Sebastian Malkusch, Alfred Ultsch
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2021.562199

Pixel-Based Machine Learning and Image Reconstitution for Dot-ELISA Pathogen Diagnosis in Biological Samples
Cited by: 1
Author(s): Cleo Anastassopoulou, Athanasios Tsakris, George P. Patrinos, Yiannis Manoussopoulos
Software Mentions: 5
Published: almost 4 years ago

10.18632/oncotarget.19662

Gene expression and molecular pathway activation signatures of<i>MYCN</i>-amplified neuroblastomas
Cited by: 27
Author(s): Ivan Petrov, Maria Suntsova, Elena Tarasovna Ilnitskaya, S. A. Roumiantsev, Maxim Sorokin, Andrew Garazha, Pavel Spirin, Timofey Lebedev, Нуршат Гайфуллин, Sergey Larin, Olga Kovalchuk, Д. М. Коновалов, Vladimir Prassolov, Alexander Roumiantsev, Anton Buzdin
Software Mentions: 5
Published: over 7 years ago

10.4269/ajtmh.19-0968

Use of Typhoid Vi-Polysaccharide Vaccine as a Vaccine Probe to Delineate Clinical Criteria for Typhoid Fever
Cited by: 0
Author(s): Tarikul Islam, Justin Im, Faisal Ahmmed, Deok Ryun Kim, Ashraful Islam Khan, Khalequ Zaman, Mohammad Ali, Florian Marks, Firdausi Qadri, Jerome H. Kim, John D. Clemens
Software Mentions: 5
Published: over 4 years ago

10.1177/0272989X16670617

Estimation of Survival Probabilities for Use in Cost-effectiveness Analyses: A Comparison of a Multi-state Modeling Survival Analysis Approach with Partitioned Survival and Markov Decision-Analytic Modeling
Cited by: 98
Author(s): Claire Williams, James Lewsey, Daniel Mackay, Andrew Briggs
Software Mentions: 5
Published: about 8 years ago

10.1186/s40462-015-0039-4

Is there a single best estimator? Selection of home range estimators using area-under-the-curve
Cited by: 68
Author(s): W. David Walter, Dave Onorato, Justin W. Fischer
Software Mentions: 5
Published: over 9 years ago

10.1002/hbm.24941

Network failures: When incentives trigger impulsive responses
Cited by: 6
Author(s): Peter Zhukovsky, Sharon Morein‐Zamir, Chun Meng, Jeffrey W. Dalley, Karen D. Ersche
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pmed.1003111

Preoperative risk stratification in endometrial cancer (ENDORISK) by a Bayesian network model: A development and validation study
Cited by: 22
Author(s): Casper Reijnen, Evangelia Gogou, Nicole C.M. Visser, Hilde Engerud, Jordache Ramjith, Louis J.M. van der Putten, Koen K. Van de Vijver, Marı́a Santacana, Peter Bronsert, Johan Bulten, Marc Hirschfeld, Eva Colás, Antonio Gil‐Moreno, Armando Reques, Gemma Mancebo, Camilla Krakstad, Jone Trovik, Ingfrid Salvesen Haldorsen, Jutta Huvila, Martin Koskas, Vít Weinberger, Markéta Bednaříková, Jitka Hausnerová, A.A.M. van der Wurff, Xavier Matías‐Guiu, Frédéric Amant, Leon F.A.G. Massuger, Marc P.L.M. Snijders, Heidi V.N. Küsters‐Vandevelde, Peter Lucas, Johanna M.A. Pijnenborg
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0068322

Reduced Incidence of Prevotella and Other Fermenters in Intestinal Microflora of Autistic Children
Cited by: 660
Author(s): Dae Wook Kang, Jin Gyoon Park, Zehra Esra Ilhan, Garrick Wallstrom, Joshua LaBaer, James B. Adams, Rosa Krajmalnik‐Brown
Software Mentions: 4
Published: over 11 years ago

10.1186/s12920-021-00960-9

Gene network analyses unveil possible molecular basis underlying drug-induced glaucoma
Cited by: 3
Author(s): Ruofan Ding, Qian Yu, Ke Liu, Juan Du, Huajun Yin, Zhi-Liang Ji
Software Mentions: 4
Published: over 3 years ago

10.1098/rsos.201622

Assessing the strength of case growth trends in the coronavirus pandemic
Cited by: 7
Author(s): Levente Kriston
Software Mentions: 4
Published: about 4 years ago

10.1093/gastro/goaa069

Nomogram to predict primary non-response to infliximab in patients with Crohn’s disease: a multicenter study
Cited by: 3
Author(s): Xiao-Qi Ye, Jing Cai, Qiao Yu, Xiaocang Cao, Yan Chen, M. K. Rao, Baili Chen, Yao He, Zhirong Zeng, Hao Chen, Yimou Lin, Qian Cao, Minhu Chen, Shenghong Zhang
Software Mentions: 4
Published: about 4 years ago

10.12688/f1000research.11823.1

Analytical challenges of untargeted GC-MS-based metabolomics and the critical issues in selecting the data processing strategy
Cited by: 19
Author(s): Ting-Li Han, Yang Yang, Hua Zhang, KT Law
Software Mentions: 4
Published: over 7 years ago

10.1007/s10329-021-00927-5

Home range size in central chimpanzees (Pan troglodytes troglodytes) from Loango National Park, Gabon
Cited by: 4
Author(s): Laura Martínez-Íñigo, Pauline Baas, Harmonie Klein, Simone Pika, Tobias Deschner
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0137112

Temporal Patterns in Seawater Quality from Dredging in Tropical Environments
Cited by: 53
Author(s): Ross Jones, Rebecca Fisher, Clair Stark, Peter V. Ridd
Software Mentions: 4
Published: about 9 years ago

10.3390/cancers10090300

Targeted UPLC-MS Metabolic Analysis of Human Faeces Reveals Novel Low-Invasive Candidate Markers for Colorectal Cancer
Cited by: 15
Author(s): Joaquín Cubiella, Marc Clos-García, Cristina Alonso, Ibon Martínez-Arránz, Miriam Pérez-Cormenzana, Ziortza Barrenetxea, J. Berganza, Isabel Rodríguez Llopis, Mauro D’Amato, Luís Bujanda, Marta Díaz‐Ondina, Juan Manuel Falcón‐Pérez
Software Mentions: 3
Published: over 6 years ago

10.1186/s12859-015-0723-9

Boosting for high-dimensional two-class prediction
Cited by: 20
Author(s): Rok Blagus, Lara Lusa
Software Mentions: 3
Published: over 9 years ago

10.1186/1472-6947-11-51

Predicting disease risks from highly imbalanced data using random forest
Cited by: 450
Author(s): Mohammed Khalilia, Suman Bhusan Chakraborty, Mihail Popescu
Software Mentions: 3
Published: over 13 years ago

10.1186/s12874-021-01340-8

Absolute mortality risk assessment of COVID-19 patients: the Khorshid COVID Cohort (KCC) study
Cited by: 5
Author(s): Hamid Reza Marateb, Maja von Cube, Ramin Sami, Shaghayegh Haghjooy Javanmard, Marjan Mansourian, Babak Amra, Forogh Soltaninejad, Mojgan Mortazavi, Peyman Adibi, Nilufar Khademi, Nastaran‐Sadat Hosseini, Arash Toghyani, Razieh Hassannejad, Miguel Ángel Mañanas, Harald Binder, Martin Wolkewitz
Software Mentions: 3
Published: over 3 years ago

10.1042/BSR20193938

Weighted gene correlation network analysis reveals novel regulatory modules associated with recurrent early pregnancy loss
Cited by: 5
Author(s): Xiaoxiao Li, Yuanqi He, Cuifang Hao, Xiaona Li, Xue Li
Software Mentions: 3
Published: over 4 years ago

10.26508/lsa.201900449

Reference-free transcriptome exploration reveals novel RNAs for prostate cancer diagnosis
Cited by: 11
Author(s): Marina Pinskaya, Zohra Saci, Mélina Gallopin, Marc Gabriel, Ha T.N. Nguyen, Virginie Firlej, Marc Descrimes, Audrey Rapinat, David Gentien, Alexandre de la Taille, Arturo Londoño-Vallejo, Yves Allory, Daniel Gautheret, Antonin Morillon
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0203449

Using dynamic Brownian Bridge Movement Models to identify home range size and movement patterns in king cobras
Cited by: 31
Author(s): Inês Silva, Matthew Crane, Pongthep Suwanwaree, Colin Thomas Strine, Matt Goode
Software Mentions: 3
Published: over 6 years ago

10.18632/aging.101102

Molecular pathway activation features of pediatric acute myeloid leukemia (AML) and acute lymphoblast leukemia (ALL) cells
Cited by: 15
Author(s): Ivan Petrov, Maria Suntsova, Olga Mutorova, Maxim Sorokin, Andrew Garazha, Elena Tarasovna Ilnitskaya, Pavel Spirin, Sergey Larin, Olga Kovalchuk, Vladimir Prassolov, Alex Zhavoronkov, Alexander Roumiantsev, Anton Buzdin
Software Mentions: 3
Published: about 8 years ago

10.3389/fmicb.2018.01913

Broad Bean (Vicia faba L.) Induces Intestinal Inflammation in Grass Carp (Ctenopharyngodon idellus C. et V) by Increasing Relative Abundances of Intestinal Gram-Negative and Flagellated Bacteria
Cited by: 12
Author(s): Zhifei Li, Ermeng Yu, Guangjun Wang, Deguang Yu, Kai Zhang, Wangbao Gong, Jun Xie
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.ppat.1008628

Timelines of infection and transmission dynamics of H1N1pdm09 in swine
Cited by: 12
Author(s): Laetitia Canini, Barbara Holzer, Sophie Morgan, Johanneke D. Hemmink, Clark Bowman, Mark Woolhouse, Elma Tchilian, Bryan Charleston
Software Mentions: 3
Published: over 4 years ago

10.1128/JVI.01787-20

Vaccines That Reduce Viral Shedding Do Not Prevent Transmission of H1N1 Pandemic 2009 Swine Influenza A Virus Infection to Unvaccinated Pigs
Cited by: 7
Author(s): Helen Everett, Pauline M. van Diemen, Mario Aramouni, Andrew Ramsay, Vivien Coward, Vincent Pavot, Laetitia Canini, Barbara Holzer, Sophie Morgan, Mark Woolhouse, Elma Tchilian, Sharon M Brookes, Ian H. Brown, Bryan Charleston, Sarah C. Gilbert
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0015850

Recursive Filtering for Zero Offset Correction of Diving Depth Time Series with GNU R Package diveMove
Cited by: 45
Author(s): S. Luque, Roland Fried
Software Mentions: 2
Published: almost 14 years ago

10.14309/ctg.0000000000000003

Plasma MicroRNA Signature Validation for Early Detection of Colorectal Cancer
Cited by: 51
Author(s): Marta Herreros-Villanueva, Saray Durán-Sanchón, Ángel G. Martín, Rosa Pérez-Palacios, Elena Vila-Navarro, María Marcuello, Mireia Diaz-Centeno, Joaquín Cubiella, Maria Soledad Diez, Luís Bujanda, Ángel Lanas, Rodrigo Jover, Vicent Hernández, Enrique Quintero, Juan José Lozano, Marta García-Cougil, Ibon Martínez-Arránz, Antoni Castells, Meritxell Gironella, Rocio Arroyo
Software Mentions: 2
Published: almost 6 years ago

10.1007/s11306-017-1164-4

Multilevel pharmacokinetics-driven modeling of metabolomics data
Cited by: 10
Author(s): Emilia Daghir-Wojtkowiak, Paweł Wiczling, Małgorzata Waszczuk-Jankowska, Roman Kaliszan, Michał J. Markuszewski
Software Mentions: 1
Published: almost 8 years ago

10.1007/s00216-020-03109-2

Benchmarking of the quantification approaches for the non-targeted screening of micropollutants and their transformation products in groundwater
Cited by: 23
Author(s): Anneli Kruve, Karin Kiefer, Juliane Hollender
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2164-8-331

Integrated analysis of independent gene expression microarray datasets improves the predictability of breast cancer outcome
Cited by: 23
Author(s): Zhe Zhang, Dechang Chen, David Fenstermacher
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2105-13-147

Arrow plot: a new graphical tool for selecting up and down regulated genes and genes differentially expressed on sample subgroups
Cited by: 17
Author(s): Carina Silva, Maria Antónia Amaral Turkman, Lisete Sousa
Software Mentions: 1
Published: over 12 years ago

10.1186/s12859-019-3288-1

Predicting effective drug combinations using gradient tree boosting based on features extracted from drug-protein heterogeneous network
Cited by: 27
Author(s): Hui Liu, Wenhao Zhang, Lei Nie, Xiancheng Ding, Judong Luo, Ling Zou
Software Mentions: 1
Published: about 5 years ago

10.3389/fonc.2021.656325

A Nomogram Model to Predict Prognosis of Patients With Genitourinary Sarcoma
Cited by: 4
Author(s): Linde Li, Jiayu Liang, Ting Song, Saifu Yin, Jun Zeng, Qiang Zhong, Xiaobing Feng, Zihao Jia, Yu Fan, Xianding Wang, Tao Lin
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2021.668761

Physicochemical Properties of Extracellular Polymeric Substances Produced by Three Bacterial Isolates From Biofouled Reverse Osmosis Membranes
Cited by: 13
Author(s): Zahid Ur Rehman, Johannes S. Vrouwenvelder, Pascal E. Saikaly
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.388

Organic carbon inventories in natural and restored Ecuadorian mangrove forests
Cited by: 28
Author(s): Amanda G. DelVecchia, John F. Bruno, Larry K. Benninger, Marc J. Alperin, Ovik Banerjee, Juan de Dios Morales
Software Mentions: 1
Published: over 10 years ago

Projects: cran: caTools

Papers Mentioning caTools 52