Data

Tools

Indexes

Applications

Experiments

Papers

Projects: cran: ggplot2

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/ggplot2

Create Elegant Data Visualisations Using the Grammar of Graphics
48 versions
Latest release: almost 3 years ago
4,921 dependent packages
2,865,232 downloads last month

Enhanced Analysis
Educational Contributors: wilke@austin.utexas.edu diggsb@ohsu.edu ruderman@usc.edu joran.elias@umontana.edu rjc2003@qatar-med.cornell.edu skopf@caltech.edu m.colombo@ed.ac.uk i.kosmidis@ucl.ac.uk melimore86@ufl.edu amurray@vt.edu nick.kennedy@ed.ac.uk dongzhuoer@mail.nankai.edu.cn benjamin.reisman@vanderbilt.edu briandk@umd.edu hye@ucsd.edu thiyanga.talagala@monash.edu brenstsr@miamioh.edu saladi@caltech.edu buyske@stat.rutgers.edu rjake@sas.upenn.edu mcmurdie@stanford.edu paul@stat.auckland.ac.nz claire.mcwhite@utexas.edu luke.mcguinness@bristol.ac.uk mdlama@wm.edu hjeppson@iastate.edu
Repository Activity:
Repository Owner: tidyverse (organization)
The tidyverse is a collection of R packages that share common principles and are designed to work together seamlessly
README Analysis:
Science Score: 100/100
Starting Score: 100 points
Bonuses:
  • +8 Academic maintainer emails
    1 maintainers with academic email addresses
  • +520 Educational commit emails
    26 contributors with educational email addresses
  • +18 Science terms in README
    9 scientific terms found in README
Very Likely Science (100)

Papers Mentioning ggplot2 11,441

10.1371/journal.pone.0216723
A metadata approach to evaluate the state of ocean knowledge: Strengths, limitations, and application to Mexico
Cited by: 10
Author(s): Juliano Palacios‐Abrantes, Andrés M. Cisneros‐Montemayor, Miguel Á. Cisneros-Mata, Laura Rodríguez, Francisco Arreguı́n-Sánchez, Verónica Aguilar, Santiago Domínguez-Sánchez, Stuart Fulton, Raquel López-Sagástegui, Héctor Reyes‐Bonilla, Rocío Rivera-Campos, Silvia Salas, Nuno Simões, William W. L. Cheung
Software Mentions: 10
Published: about 7 years ago
10.1038/s42003-021-02407-4
Social familiarity improves fast-start escape performance in schooling fish
Cited by: 8
Author(s): Lauren E. Nadler, Mark I. McCormick, Jacob L. Johansen, Paolo Domenici
Software Mentions: 10
Published: about 5 years ago
10.1128/mSystems.00571-21
Pathogenic <i>Vibrio</i> Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes
Cited by: 11
Author(s): Rachel E. Diner, Drishti Kaul, Ariel Rabines, Hong Zheng, Joshua A. Steele, John F. Griffith, Andrew E. Allen
Software Mentions: 10
Published: almost 5 years ago
10.3390/v12111229
RNAseq of Deformed Wing Virus and Other Honey Bee-Associated Viruses in Eight Insect Taxa with or without Varroa Infestation
Cited by: 17
Author(s): Laura E. Brettell, Declan C. Schroeder, Stephen J. Martin
Software Mentions: 10
Published: almost 6 years ago
10.1371/journal.pone.0185171
Interactions affect hyphal growth and enzyme profiles in combinations of coniferous wood-decaying fungi of Agaricomycetes
Cited by: 29
Author(s): Tuulia Mali, Jaana Kuuskeri, Firoz Shah, Taina Lundell
Software Mentions: 10
Published: almost 9 years ago
10.3389/fmicb.2020.00037
FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies
Cited by: 164
Author(s): Arkadiy I. Garber, Kenneth H. Nealson, Akimitsu Okamoto, Sean M. McAllister, Clara S. Chan, Roman A. Barco, Nancy Merino
Software Mentions: 10
Published: over 6 years ago
10.1534/g3.120.401309
CeMbio - The<i>Caenorhabditis elegans</i>Microbiome Resource
Cited by: 71
Author(s): Philipp Dirksen, Adrien Assié, Johannes Zimmermann, Fan Zhang, Adina-Malin Tietje, Sarah Arnaud Marsh, Marie‐Anne Félix, Michael Y. Shapira, Christoph Kaleta, Hinrich Schulenburg, Buck S. Samuel
Software Mentions: 10
Published: almost 6 years ago
10.1038/s41598-020-71663-x
Discovering the indigenous microbial communities associated with the natural fermentation of sap from the cider gum Eucalyptus gunnii
Cited by: 12
Author(s): Cristián Varela, Joanna F. Sundstrom, Kathleen Cuijvers, Vladimir Jiranek, Anthony R. Borneman
Software Mentions: 10
Published: almost 6 years ago
10.1038/s42003-019-0646-5
Histone acetylation orchestrates wound-induced transcriptional activation and cellular reprogramming in Arabidopsis
Cited by: 59
Author(s): Bart Rymen, Ayako Kawamura, Alice Lambolez, Soichi Inagaki, Arika Takebayashi, Akira Iwase, Yuki Sakamoto, Kaori Sako, David S. Favero, Momoko Ikeuchi, Takamasa Suzuki, Masanori Seki, Tetsuji Kakutani, François Roudier, Keiko Sugimoto
Software Mentions: 10
Published: over 6 years ago
10.1093/iob/obaa024
The Balance Hypothesis for the Avian Lumbosacral Organ and an Exploration of Its Morphological Variation
Cited by: 11
Author(s): Kathryn E Stanchak, C. French, David J. Perkel, Bingni W. Brunton
Software Mentions: 10
Published: over 6 years ago
10.1038/s41598-021-96236-4
A novel prognostic signature of immune-related lncRNA pairs in lung adenocarcinoma
Cited by: 5
Author(s): Yang Liu, Qiuhong Wu, Xuejiao Fan, Wen Li, Yong Li, Hui Zhu, Qinghua Zhou, Jinming Yu
Software Mentions: 10
Published: almost 5 years ago
10.3389/fgene.2021.695130
A Novel Signature Constructed by Immune-Related LncRNA Predicts the Immune Landscape of Colorectal Cancer
Cited by: 7
Author(s): Mengyu Sun, Tongyue Zhang, Yijun Wang, Wenjie Huang, Limin Xia
Software Mentions: 10
Published: almost 5 years ago
10.7554/eLife.66036
A new Heterodontosaurus specimen elucidates the unique ventilatory macroevolution of ornithischian dinosaurs
Cited by: 8
Author(s): Viktor J. Radermacher, Vincent Fernández, Emma R. Schachner, Richard J. Butler, Emese M. Bordy, Michael Naylor Hudgins, William J. De Klerk, Kimberley E. J. Chapelle, Jonah N. Choiniere
Software Mentions: 10
Published: about 5 years ago
10.1038/s41396-020-00862-1
Fungal sporocarps house diverse and host-specific communities of fungicolous fungi
Cited by: 21
Author(s): Sundy Maurice, Gontran Arnault, Jenni Nordén, Synnøve Smebye Botnen, Otto Miettinen, Håvard Kauserud
Software Mentions: 10
Published: over 5 years ago
10.1093/bioinformatics/btv428
dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering
Cited by: 1,079
Author(s): Tal Galili
Software Mentions: 10
Published: about 11 years ago
10.3389/fmicb.2020.597745
Impact of Long-Term Organic and Mineral Fertilization on Rhizosphere Metabolites, Root–Microbial Interactions and Plant Health of Lettuce
Cited by: 15
Author(s): Saskia Windisch, Loreen Sommermann, Doreen Babin, Soumitra Paul Chowdhury, Rita Grosch, Narges Moradtalab, Frank Walker, Birgit Höglinger, Abbas El‐Hasan, Wolfgang Armbruster, Joseph Nesme, Søren J. Sørensen, Ingo Schellenberg, Joerg Geistlinger, Kornelia Smalla, Michael Rothballer, Uwe Ludewig, Günter Neumann
Software Mentions: 10
Published: over 5 years ago
10.1186/s40168-020-00895-w
Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota
Cited by: 32
Author(s): Shashank Gupta, Mathis Hjort Hjelmsø, Jenni Lehtimäki, Xuanji Li, Martin Steen Mortensen, Jakob Russel, Urvish Trivedi, Morten Arendt Rasmussen, Jakob Stokholm, Hans Bisgaard, Søren J. Sørensen
Software Mentions: 10
Published: almost 6 years ago
10.1038/s41598-020-72369-w
Connectivity and population structure of albacore tuna across southeast Atlantic and southwest Indian Oceans inferred from multidisciplinary methodology
Cited by: 10
Author(s): Natacha Nikolic, Iratxe Montes, Maxime Lalire, Alexis Puech, Nathalie Bodin, Sophie Arnaud‐Haond, Sven E. Kerwath, Emmanuel Corse, Philippe Gaspar, Stéphanie Hollanda, Jérôme Bourjea, Wendy West, Sylvain Bonhommeau
Software Mentions: 10
Published: almost 6 years ago
10.3389/fcell.2021.731790
Identification and Validation of a Nine-Gene Amino Acid Metabolism-Related Risk Signature in HCC
Cited by: 34
Author(s): Yajuan Zhao, Junli Zhang, Shuhan Wang, Qianqian Jiang, Ke Xu
Software Mentions: 10
Published: almost 5 years ago
10.1186/s12940-021-00693-3
Examining the role of wind in human illness due to pesticide drift in Washington state, 2000–2015
Cited by: 3
Author(s): Edward J. Kasner, Joanne Bonnar Prado, Michael G. Yost, Richard A. Fenske
Software Mentions: 10
Published: over 5 years ago
10.1017/S0950268820000746
Risk of bacteremia in patients presenting with shaking chills and vomiting - a prospective cohort study
Cited by: 2
Author(s): Madlene Holmqvist, Malin Inghammar, Lisa I. Påhlman, John H. Boyd, Per Åkesson, Adam Linder, Fredrik Kahn
Software Mentions: 10
Published: over 6 years ago
10.7554/eLife.43257
Beta-catenin signaling regulates barrier-specific gene expression in circumventricular organ and ocular vasculatures
Cited by: 65
Author(s): Yanshu Wang, Mark F Sabbagh, Xiaowu Gu, Amir Rattner, John Williams, Jeremy Nathans
Software Mentions: 10
Published: over 7 years ago
10.3390/cancers13133371
Meta-Analysis of Microdissected Breast Tumors Reveals Genes Regulated in the Stroma but Hidden in Bulk Analysis
Cited by: 7
Author(s): Aurora Savino, Niccolò De Marzo, Paolo Provero, Valeria Poli
Software Mentions: 10
Published: about 5 years ago
10.3389/fmicb.2020.00917
Changes in Faecal Microbiota Profiles Associated With Performance and Birthweight of Piglets
Cited by: 23
Author(s): Clare H. Gaukroger, Christopher J. Stewart, Sandra Edwards, John Walshaw, Ian Adams, Ι. Kyriazakis
Software Mentions: 10
Published: about 6 years ago
10.1038/s42003-020-1087-x
Combining host-derived biomarkers with patient characteristics improves signature performance in predicting tuberculosis treatment outcomes
Cited by: 12
Author(s): Dhanasekaran Sivakumaran, Synne Jenum, Mário Vaz, Sumithra Selvam, Tom H. M. Ottenhoff, Mariëlle C. Haks, Stephanus T. Malherbe, Nancy Devlin, Christian Ritz, Harleen M. S. Grewal
Software Mentions: 10
Published: about 6 years ago
10.1371/journal.pntd.0008934
An investig-ation into the epidemiology of chikungunya virus across neglected regions of Indonesia
Cited by: 6
Author(s): Sam Stubbs, Edison Johar, Frilasita A. Yudhaputri, Benediktus Yohan, Marsha S. Santoso, Rahma Hayati, Dionisius Denis, Barbara Blacklaws, Ann M. Powers, R. Tedjo Sasmono, Khin Saw Aye Myint, Simon D. W. Frost
Software Mentions: 10
Published: over 5 years ago
10.3390/cancers13020230
A Set of Cell Lines Derived from a Genetic Murine Glioblastoma Model Recapitulates Molecular and Morphological Characteristics of Human Tumors
Cited by: 10
Author(s): Bárbara Costa, Michael Fletcher, Pavle Boskovic, Ekaterina Ivanova, Tanja Eisemann, Sabrina Lohr, Lukas Bunse, Martin Löwer, Stefanie Burchard, Andrey Korshunov, Nadia Coltella, Melania Cusimano, Luigi Naldini, Hai-Kun Liu, Michael Platten, Bernhard Radlwimmer, Peter Angel, Heike Peterziel
Software Mentions: 10
Published: over 5 years ago
10.1186/s12916-020-01595-w
Serum metabolite profiles are associated with the presence of advanced liver fibrosis in Chinese patients with chronic hepatitis B viral infection
Cited by: 30
Author(s): Guoxiang Xie, Xiaoning Wang, Runmin Wei, Jingye Wang, Aihua Zhao, Tianlu Chen, Yixing Wang, Hua Zhang, Zhun Xiao, Xin-Zhu Liu, Youping Deng, Linda L. Wong, Cynthia Rajani, Sandi A. Kwee, Hua Bian, Xin Gao, Ping Liu, Jia Wang
Software Mentions: 10
Published: about 6 years ago
10.1186/s40462-019-0175-3
Exploration during early life: distribution, habitat and orientation preferences in juvenile king penguins
Cited by: 14
Author(s): Florian Orgeret, Clara Péron, Manfred R. Enstipp, Karine Delord, Henri Weimerskirch, CA Bost
Software Mentions: 10
Published: almost 7 years ago
10.1371/journal.pgen.1008530
Genetic variation in GC and CYP2R1 affects 25-hydroxyvitamin D concentration and skeletal parameters: A genome-wide association study in 24-month-old Finnish children
Cited by: 12
Author(s): Anders Kämpe, Maria Enlund-Cerullo, Saara Valkama, Elisa Holmlund-Suila, Jenni Rosendahl, Helena Hauta-alus, Minna Pekkinen, Sture Andersson, Outi Mäkitie
Software Mentions: 10
Published: over 6 years ago
10.1007/s00125-018-4641-z
Multiplex proteomics for prediction of major cardiovascular events in type 2 diabetes
Cited by: 38
Author(s): Christoph Nowak, Axel C. Carlsson, Carl Johan Östgren, Fredrik Nyström, Moudud Alam, Tobias Feldreich, Johan Sundström, Juan-Jesús Carrero, Jerzy Leppert, Pär Hedberg, Egil Henriksen, A. C. C. Cordeiro, Vilmantas Giedraitis, Lars Lind, Erik Ingelsson, Tove Fall, Johan Ärnlöv
Software Mentions: 10
Published: about 8 years ago
10.1093/molbev/msu269
Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci
Cited by: 488
Author(s): Simon H. Martin, John W. Davey, Chris D. Jiggins
Software Mentions: 10
Published: almost 12 years ago
10.3389/fvets.2020.00604
Autoregressive Models Applied to Time-Series Data in Veterinary Science
Cited by: 9
Author(s): Michael P. Ward, Rachel M Iglesias, Victoria Brookes
Software Mentions: 10
Published: almost 6 years ago
10.1186/s13059-018-1432-2
FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map
Cited by: 57
Author(s): Tom Aharon Hait, David Amar, Ron Shamir, Ran Elkon
Software Mentions: 10
Published: over 8 years ago
10.1242/dev.193060
Extensive nuclear gyration and pervasive non-genic transcription during primordial germ cell development in zebrafish
Cited by: 4
Author(s): Stefan Redl, António Miguel de Jesus Domingues, Edoardo Caspani, Stefanie Möckel, Willi Salvenmoser, María Méndez-Lago, René F. Ketting
Software Mentions: 10
Published: over 6 years ago
10.1155/2021/7404927
A Comprehensive Multiomics Analysis Identified Ubiquilin 4 as a Promising Prognostic Biomarker of Immune-Related Therapy in Pan-Cancer
Cited by: 4
Author(s): Jie Li, Ye Tong, Zhi Wang, Yi Liu, Xiaofeng Dai, Yubing Zhu
Software Mentions: 10
Published: almost 5 years ago
10.1186/s12859-021-03967-2
tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R
Cited by: 7
Author(s): Charlie M. Carpenter, Daniel N. Frank, Kayla Williamson, Jaron Arbet, Brandie D. Wagner, Katerina Kechris, Miranda Kroehl
Software Mentions: 10
Published: over 5 years ago
10.1371/journal.pgen.1008126
Identification of novel genes involved in phosphate accumulation in Lotus japonicus through Genome Wide Association mapping of root system architecture and anion content
Cited by: 14
Author(s): Marco Giovannetti, Christian Göschl, Christof Dietzen, Stig Uggerhøj Andersen, Stanislav Kopriva, Wolfgang Busch
Software Mentions: 10
Published: over 6 years ago
10.18632/aging.203257
Characterization of ferroptosis signature to evaluate the predict prognosis and immunotherapy in glioblastoma
Cited by: 14
Author(s): Xiaopeng Zhu, Yuxiang Zhou, Yangqian Ou, Zebo Cheng, Deqing Han, Zhou Chu, Sian Pan
Software Mentions: 10
Published: about 5 years ago
10.1155/2017/7457131
NFP: An R Package for Characterizing and Comparing of Annotated Biological Networks
Cited by: 0
Author(s): Yang Cao, Wenjian Xu, Chao Niu, Xiaochen Bo, Fēi Li
Software Mentions: 10
Published: over 9 years ago
10.1186/s12920-020-00754-5
Identification of potential crucial genes in atrial fibrillation: a bioinformatic analysis
Cited by: 15
Author(s): Junguo Zhang, Xin Huang, Xiaojie Wang, Yanhui Gao, Li Liu, Ziyi Li, Xuejiao Chen, Jie Zeng, Zebing Ye, Guowei Li
Software Mentions: 10
Published: about 6 years ago
10.1093/database/bay033
The tragedy of the biodiversity data commons: a data impediment creeping nigher?
Cited by: 11
Author(s): Nora Escribano, David Galicia, Arturo H. Ariño
Software Mentions: 10
Published: over 8 years ago
10.1186/s11689-021-09360-7
Modeling familial predictors of proband outcomes in neurogenetic disorders: initial application in XYY syndrome
Cited by: 3
Author(s): Kathleen Wilson, Ari M. Fish, Catherine Mankiw, Anastasia Xenophontos, Allysa Warling, Ethan T. Whitman, Liv S. Clasen, Erin Torres, Jonathan D. Blumenthal, Armin Raznahan
Software Mentions: 10
Published: over 5 years ago
10.1371/journal.pgen.1008831
Behavioral and brain- transcriptomic synchronization between the two opponents of a fighting pair of the fish Betta splendens
Cited by: 18
Author(s): Trieu-Duc Vu, Yoshiaki Iwasaki, Shuji Shigenobu, Akiko Maruko, Koichiro Oshima, Erica Iioka, Chao Li Huang, Takashi Abe, Satoshi Tamaki, Yi-Sheng Lin, Chih Kuan Chen, Mei-Yeh Jade Lu, Masaru Hojo, Hao Ven Wang, Shun Fen Tzeng, Hao Huang, Akio Kanai, Takashi Gojobori, Tzen‐Yuh Chiang, Han Sun, Wen-Hsiung Li, Norihiro Okada
Software Mentions: 10
Published: about 6 years ago
10.3389/fneur.2021.683051
An Externally Validated Dynamic Nomogram for Predicting Unfavorable Prognosis in Patients With Aneurysmal Subarachnoid Hemorrhage
Cited by: 8
Author(s): Ping Hu, Yang Xu, Yangfan Liu, Yuntao Li, Liguo Ye, Si Zhang, Xinyi Zhu, Yangzhi Qi, Huikai Zhang, Qian Sun, Yixuan Wang, Gang Deng, Qianxue Chen
Software Mentions: 10
Published: almost 5 years ago
10.1155/2021/6365459
Identification of a Pyroptosis-Related Gene Signature for Prediction of Overall Survival in Lung Adenocarcinoma
Cited by: 14
Author(s): Donghai Zheng, Lv Bian, Minglang Wang, Luoqing Wang, Yilian Wang
Software Mentions: 10
Published: almost 5 years ago
10.1186/s42523-021-00094-4
Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scales
Cited by: 23
Author(s): Connie A. Rojas, Santiago Ramírez‐Barahona, Kay E. Holekamp, Kevin R. Theis
Software Mentions: 10
Published: over 5 years ago
10.3390/microorganisms9071487
Changes in Skin and Nasal Microbiome and Staphylococcal Species Following Treatment of Atopic Dermatitis with Dupilumab
Cited by: 20
Author(s): Caroline Meyer Olesen, Anna Cäcilia Ingham, Simon Francis Thomsen, Maja‐Lisa Clausen, Paal Skytt Andersen, Sofie Marie Edslev, Yasemin Topal Yüksel, Emma Guttman‐Yassky, Tove Agner
Software Mentions: 10
Published: about 5 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: about 11 years ago
10.3390/ijms22179601
In Silico Methods for the Identification of Diagnostic and Favorable Prognostic Markers in Acute Myeloid Leukemia
Cited by: 7
Author(s): Hande Öngün Yılmaz, Halil Ibrahim Toy, Stephan Marquardt, Gökhan Karakülah, Can Küçük, Panagiota I. Kontou, Stella Logotheti, Athanasia Pavlopoulou
Software Mentions: 10
Published: almost 5 years ago
10.7554/eLife.32073
Destructive disinfection of infected brood prevents systemic disease spread in ant colonies
Cited by: 69
Author(s): Christopher D. Pull, Line V. Ugelvig, Florian Wiesenhofer, Anna V. Grasse, Simon Tragust, Thomas Schmitt, Mark J. F. Brown, Sylvia Cremer
Software Mentions: 10
Published: over 8 years ago
10.1186/s12859-020-03549-8
BEAVR: a browser-based tool for the exploration and visualization of RNA-seq data
Cited by: 12
Author(s): Pirunthan Perampalam, Frederick A. Dick
Software Mentions: 10
Published: about 6 years ago
10.1371/journal.pgen.1008458
Microbial phenotypic heterogeneity in response to a metabolic toxin: Continuous, dynamically shifting distribution of formaldehyde tolerance in Methylobacterium extorquens populations
Cited by: 23
Author(s): Jessica A. Lee, Siavash Riazi, Shahla Nemati, Jannell V. Bazurto, Andreas E. Vasdekis, Benjamin J. Ridenhour, Christopher H. Remien, Christopher J. Marx
Software Mentions: 10
Published: over 6 years ago
10.3390/ijms20061510
Placenta Transcriptome Profiling in Intrauterine Growth Restriction (IUGR)
Cited by: 48
Author(s): Marta Majewska, Aleksandra Lipka, Łukasz Paukszto, J Jastrzebski, Karol Szeszko, Marek Gowkielewicz, Ewa Lepiarczyk, Marcin Jóźwik, Mariusz Majewski
Software Mentions: 10
Published: over 7 years ago
10.3389/fgene.2018.00461
TEsmall Identifies Small RNAs Associated With Targeted Inhibitor Resistance in Melanoma
Cited by: 4
Author(s): Kathryn O’Neill, Wen‐Wei Liao, Asmita Patel, Molly Gale Hammell
Software Mentions: 10
Published: almost 8 years ago
10.7554/eLife.10421
Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain
Cited by: 115
Author(s): Claudia Scheckel, Elodie Drapeau, María A. Frías, Christopher Y. Park, John Fak, Ilana Zucker-Scharff, Yan Kou, Vahram Haroutunian, Avi Ma’ayan, Joseph D. Buxbaum, Robert B. Darnell
Software Mentions: 10
Published: over 10 years ago
10.3389/fonc.2020.526577
Patient Stratification of Clear Cell Renal Cell Carcinoma Using the Global Transcription Factor Activity Landscape Derived From RNA-Seq Data
Cited by: 7
Author(s): Yanyan Zhu, Shundong Cang, Bowang Chen, Ye Gu, Miaomiao Jiang, Junya Yan, Fengmin Shao, Xiaoyun Huang
Software Mentions: 10
Published: over 5 years ago
10.7554/eLife.62210
Proteomic analysis of young and old mouse hematopoietic stem cells and their progenitors reveals post-transcriptional regulation in stem cells
Cited by: 18
Author(s): Balyn W. Zaro, Joseph J. Noh, Victoria L. Mascetti, János Demeter, Benson M. George, Monika Żukowska, Gunsagar S. Gulati, Rahul Sinha, Ryan A. Flynn, Allison Banuelos, Allison Zhang, Adam C. Wilkinson, Peter K. Jackson, Irving L. Weissman
Software Mentions: 10
Published: over 5 years ago
10.2196/26412
Recursive partitioning vs computerized adaptive testing to reduce the burden of health assessment in cleft lip and/or palate: a comparative simulation study (Preprint)
Cited by: 1
Author(s): Conrad Harrison, Chris Sidey‐Gibbons, Anne F. Klassen, Karen W. Y. Wong Riff, Dominic Furniss, Marc C. Swan, Jeremy Rodrigues
Software Mentions: 10
Published: over 5 years ago
10.1007/s10456-020-09743-9
Epigenetic regulation of the lineage specificity of primary human dermal lymphatic and blood vascular endothelial cells
Cited by: 16
Author(s): Carlotta Tacconi, Yuliang He, Luca Ducoli, Michael Detmar
Software Mentions: 10
Published: almost 6 years ago
10.3389/fonc.2020.01710
Prognostic Implications of Metabolism Related Gene Signature in Cutaneous Melanoma
Cited by: 14
Author(s): Furong Zeng, Juan Su, Cong Peng, Mengting Liao, Shuang Zhao, Ying Guo, Xiang Chen, Guangtong Deng
Software Mentions: 10
Published: almost 6 years ago
10.3389/fgene.2019.00279
Integrative Differential Expression Analysis for Multiple EXperiments (IDEAMEX): A Web Server Tool for Integrated RNA-Seq Data Analysis
Cited by: 46
Author(s): Verónica Jiménez-Jacinto, Alejandro Sánchez-Flores, Leticia Vega‐Alvarado
Software Mentions: 10
Published: over 7 years ago
10.1155/2020/5858092
Profiles of Immune Infiltration and Prognostic Immunoscore in Lung Adenocarcinoma
Cited by: 9
Author(s): Yanyan Li, Liping Tao, Weiyang Cai
Software Mentions: 10
Published: about 6 years ago
10.7554/eLife.36187
Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells
Cited by: 167
Author(s): Mark F Sabbagh, Jacob S Heng, Chongyuan Luo, Rosa Castanon, Joseph R. Nery, Amir Rattner, Loyal A. Goff, Joseph R. Ecker, Jeremy Nathans
Software Mentions: 10
Published: almost 8 years ago
10.1371/journal.pgen.1009376
Histone modification dynamics at H3K27 are associated with altered transcription of in planta induced genes in Magnaporthe oryzae
Cited by: 46
Author(s): Wei Zhang, Jun Huang, David E. Cook
Software Mentions: 10
Published: over 5 years ago
10.1186/s12864-015-2250-5
Leveraging global gene expression patterns to predict expression of unmeasured genes
Cited by: 3
Author(s): James Rudd, René A. Zelaya, Eugene Demidenko, Ellen L. Goode, Casey S. Greene, Jennifer A. Doherty
Software Mentions: 10
Published: over 10 years ago
10.3390/ijerph18168271
Cluster Analysis of Urban Acoustic Environments on Barcelona Sensor Network Data
Cited by: 10
Author(s): Antonio Pita, Francisco Javier Iglesias Rodríguez, Juan M. Navarro
Software Mentions: 10
Published: almost 5 years ago
10.3389/fmicb.2019.02476
Characterization of the Mycobiome of the Seagrass, Zostera marina, Reveals Putative Associations With Marine Chytrids
Cited by: 29
Author(s): Cassandra L. Ettinger, Jonathan A. Eisen
Software Mentions: 10
Published: over 6 years ago
10.1371/journal.pcbi.1009380
Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants
Cited by: 11
Author(s): Rui Yin, Johnathan D. Guest, Ghazaleh Taherzadeh, Ragul Gowthaman, Ipsa Mittra, Jane Quackenbush, Brian G. Pierce
Software Mentions: 10
Published: almost 5 years ago
10.1371/journal.pcbi.1007803
Methodological challenges in translational drug response modeling in cancer: A systematic analysis with FORESEE
Cited by: 9
Author(s): Lisa-Katrin Turnhoff, Ali Hadizadeh Esfahani, Andreas Schuppert
Software Mentions: 10
Published: over 6 years ago
10.1007/s00401-020-02224-9
Altered DNA methylation profiles in blood from patients with sporadic Creutzfeldt–Jakob disease
Cited by: 14
Author(s): Luke C. Dabin, Fernando Guntoro, Tracy Campbell, Tony Bélicard, Adam R. Smith, Rebecca G. Smith, Rachel Raybould, Jonathan M. Schott, Katie Lunnon, Peter Sarkies, John Collinge, Simon Mead, Emmanuelle Viré
Software Mentions: 10
Published: almost 6 years ago
10.7717/peerj.11903
Taxonomic and functional diversity of benthic macrofauna associated with rhodolith beds in SE Brazil
Cited by: 10
Author(s): Patricia Sarcinelli Stelzer, Ana Carolina de Azevedo Mazzuco, L.E. de O. Gomes, João Luiz Martins, Sérgio A. Netto, Ângelo F. Bernardino
Software Mentions: 10
Published: about 5 years ago
10.1128/mSphere.00743-20
Whole-Genome Sequence Analysis of an Extensively Drug-Resistant Salmonella enterica Serovar Agona Isolate from an Australian Silver Gull ( <i>Chroicocephalus novaehollandiae</i> ) Reveals the Acquisition of Multidrug Resistance Plasmids
Cited by: 17
Author(s): Max L. Cummins, Martina L. Sanderson-Smith, Peter Newton, Nicholas Carlile, David N. Phalen, Kimberly Maute, Leigh G. Monahan, Bethany J. Hoye, Steven P. Djordjevic
Software Mentions: 10
Published: over 5 years ago
10.3389/fmolb.2021.692530
Ferroptosis-Related Gene Signature and Patterns of Immune Infiltration Predict the Overall Survival in Patients With Lung Adenocarcinoma
Cited by: 5
Author(s): Yuxuan Wang, Weikang Chen, Minqi Zhu, Lei Xian
Software Mentions: 10
Published: about 5 years ago
10.18632/aging.102434
Development and validation of a metastasis-associated prognostic signature based on single-cell RNA-seq in clear cell renal cell carcinoma
Cited by: 28
Author(s): Chuanjie Zhang, Hongchao He, Xin Hu, Ao Liu, Da Huang, Yu Xu, Lu Chen, Danfeng Xu
Software Mentions: 10
Published: over 6 years ago
10.1186/s12864-021-07388-6
Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential
Cited by: 3
Author(s): Niels A. Zondervan, Vítor A. P. Martins dos Santos, María Suárez-Diez, Edoardo Saccenti
Software Mentions: 10
Published: over 5 years ago
10.1186/s12864-015-2356-9
QuickRNASeq lifts large-scale RNA-seq data analyses to the next level of automation and interactive visualization
Cited by: 33
Author(s): Shanrong Zhao, Li Xi, Jie Quan, Hualin Simon Xi, Ying Zhang, David von Schack, Michael S. Vincent, Baohong Zhang
Software Mentions: 10
Published: over 10 years ago
10.1097/MD.0000000000026068
MiRNA-based model for predicting the TMB level in colon adenocarcinoma based on a LASSO logistic regression method
Cited by: 1
Author(s): Zhengtian Li, Lingling Jiang, Rong Zhao, Jun Huang, Weibo Yang, Zhenpei Wen, Bo Zhang, Gang Du
Software Mentions: 10
Published: about 5 years ago
10.7717/peerj.10264
MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information
Cited by: 6
Author(s): Elly Poretsky, Alisa Huffaker
Software Mentions: 10
Published: over 5 years ago
10.1038/s41598-021-94329-8
Combined detection of peripheral blood VEGF and inflammation biomarkers to evaluate the clinical response and prognostic prediction of non-operative ESCC
Cited by: 4
Author(s): Yuanyuan Ma, Xinyu Su, Xin Li, Xiaohui Zhi, Kan Jiang, Jianhong Xia, Hongliang Li, Yan Chen, Lixin Zhou
Software Mentions: 10
Published: about 5 years ago
10.1038/s41598-020-76103-4
Phenotypic variation, functional traits repeatability and core collection inference in Synsepalum dulcificum (Schumach &amp; Thonn.) Daniell reveals the Dahomey Gap as a centre of diversity
Cited by: 3
Author(s): Dèdéou Apocalypse Tchokponhoué, Enoch G. Achigan‐Dako, Sognigbé N’Danikou, Daniel Nyadanu, Rémi Kahane, Jacob S Houéto, V.N. Fassinou Hotegni, Alfred Odindo, Julia Sibiya
Software Mentions: 10
Published: over 5 years ago
10.1038/s41598-021-89904-y
Feasibility of predicting allele specific expression from DNA sequencing using machine learning
Cited by: 5
Author(s): Zhenhua Zhang, Freerk van Dijk, Nigel Klein, Mariëlle van Gijn, Lude Franke, Richard J. Sinke, Morris A. Swertz, K. Joeri van der Velde
Software Mentions: 10
Published: about 5 years ago
10.18632/aging.202174
Periodontitis in elderly patients with type 2 diabetes mellitus: impact on gut microbiota and systemic inflammation
Cited by: 18
Author(s): Jinyou Li, Haifeng Lü, Hengchao Wu, Shunmei Huang, Lufang Chen, Qifeng Gui, Wenjing Zhou, Yichen Yang, Yue Wu, Hua Zhang, Qin Zhang, Yunmei Yang
Software Mentions: 10
Published: over 5 years ago
10.7717/peerj.8027
Limited initial impacts of biomass harvesting on composition of wood-inhabiting fungi within residual stumps
Cited by: 0
Author(s): Cédric Boué, Tonia DeBellis, Lisa Venier, Timothy T. Work, Steven W. Kembel
Software Mentions: 10
Published: over 6 years ago
10.1002/ece3.4550
Size does matter: Parallel evolution of adaptive thermal tolerance and body size facilitates adaptation to climate change in domestic cattle
Cited by: 20
Author(s): Muhammed Elayadeth-Meethal, Aravindakshan Thazhathu Veettil, Shane K. Maloney, N. J. Hawkins, Tom Misselbrook, Veerasamy Sejian, M. Jordana Rivero, Michael R. F. Lee
Software Mentions: 10
Published: almost 8 years ago
10.3389/fimmu.2021.722860
Transcriptional Changes in Regulatory T Cells From Patients With Autoimmune Polyendocrine Syndrome Type 1 Suggest Functional Impairment of Lipid Metabolism and Gut Homing
Cited by: 1
Author(s): A Berger, Eirik Bratland, Thea Sjøgren, Marte Heimli, Torgeir Tyssedal, Øyvind Bruserud, Stefan Johansson, Eystein S. Husebye, Bergithe E. Oftedal, Anette Susanne Bøe Wolff
Software Mentions: 10
Published: almost 5 years ago
10.7717/peerj.10421
Loss of HOXB3 correlates with the development of hormone receptor negative breast cancer
Cited by: 6
Author(s): Lizhe Zhu, Shibo Yu, Siyuan Jiang, Ge Gao, Yan Yu, Yong Jin Zhou, Ligang Niu, Jing He, Yu Ren, Bin Wang
Software Mentions: 10
Published: over 5 years ago
10.1038/s41598-020-78228-y
Gastrointestinal adenocarcinoma analysis identifies promoter methylation-based cancer subtypes and signatures
Cited by: 7
Author(s): Renshen Xiang, Tao Fu
Software Mentions: 10
Published: over 5 years ago
10.1186/s13059-014-0413-3
A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators
Cited by: 19
Author(s): Laurence D. Hurst, Oxana Sachenkova, Carsten O. Daub, Alistair R.R. Forrest, Łukasz Huminiecki
Software Mentions: 10
Published: about 12 years ago
10.1111/jcmm.16619
Systematic profiling of invasion‐related gene signature predicts prognostic features of lung adenocarcinoma
Cited by: 17
Author(s): Ping Yu, L. Tong, Yujia Song, Hui Qü, Ying Chen
Software Mentions: 10
Published: about 5 years ago
10.1038/s41598-020-74909-w
Multi-strain volatile profiling of pathogenic and commensal cutaneous bacteria
Cited by: 19
Author(s): Shane Fitzgerald, Emer Duffy, Linda Holland, Aoife Morrin
Software Mentions: 10
Published: almost 6 years ago
10.1371/journal.pone.0215142
Mathematical modeling for the prediction of cerebral white matter lesions based on clinical examination data
Cited by: 7
Author(s): Yuya Shinkawa, Takashi Yoshida, Yohei Onaka, Makoto Ichinose, Kazuo Ishii
Software Mentions: 10
Published: over 7 years ago
10.1371/journal.pone.0209331
Rethomics: An R framework to analyse high-throughput behavioural data
Cited by: 66
Author(s): Quentin Geissmann, Luis García Rodríguez, Esteban J. Beckwith, Giorgio F. Gilestro
Software Mentions: 10
Published: over 7 years ago
10.1038/s41598-020-65160-4
Influence of climate variation on phenolic composition and antioxidant capacity of Medicago minima populations
Cited by: 45
Author(s): Souhir Kabtni, Dorra Sdouga, Ines Bettaib Rebey, Mattew Save, Neïla Trifi-Farah, Marie‐Laure Fauconnier, Sonia Marghali
Software Mentions: 10
Published: about 6 years ago
10.1186/s12864-019-6181-4
Dynamic transcriptome sequencing and analysis during early development in the bighead carp (Hypophthalmichthys nobilis)
Cited by: 12
Author(s): Jianjun Fu, Wenbin Zhu, Lanmei Wang, Ming Luo, Fei Song, Zaijie Dong
Software Mentions: 10
Published: almost 7 years ago
10.1186/s40360-021-00505-x
Causal inference multiple imputation investigation of the impact of cannabinoids and other substances on ethnic differentials in US testicular cancer incidence
Cited by: 26
Author(s): Albert Stuart Reece, Gary Kenneth Hulse
Software Mentions: 10
Published: about 5 years ago
10.3389/fgene.2020.00260
IntAssoPlot: An R Package for Integrated Visualization of Genome-Wide Association Study Results With Gene Structure and Linkage Disequilibrium Matrix
Cited by: 20
Author(s): Fengyu He, Shuangcheng Ding, Hongwei Wang, Feng Qin
Software Mentions: 10
Published: over 6 years ago
10.3389/fmicb.2021.706214
Dietary Exposure of Pacific Oyster (Crassostrea gigas) Larvae to Compromised Microalgae Results in Impaired Fitness and Microbiome Shift
Cited by: 5
Author(s): Julien Vignier, Olivier Laroche, Anne Rolton, Pandora Wadsworth, K. Kumanan, Branwen Trochel, Xavier Pochon, Nathan King
Software Mentions: 10
Published: almost 5 years ago
10.3389/fgene.2021.682475
Genomic and Chemical Diversity of Commercially Available High-CBD Industrial Hemp Accessions
Cited by: 10
Author(s): Matthew Johnson, Jason Wallace
Software Mentions: 10
Published: about 5 years ago
10.3389/fmicb.2021.642543
Patterns of Microbiome Variation Among Infrapopulations of Permanent Bloodsucking Parasites
Cited by: 6
Author(s): Jorge Doña, Stephany Virrueta Herrera, Tommi Nyman, Mervi Kunnasranta, Kevin P. Johnson
Software Mentions: 10
Published: over 5 years ago