cran: tibble | Projects | Ecosyste.ms: Papers

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: almost 5 years ago

An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates
Cited by: 61
Author(s): Arun Gonzales Decano, Tim Downing
Software Mentions: 30
Published: almost 5 years ago

10.1084/jem.20210915

Blood transcriptomics reveal the evolution and resolution of the immune response in tuberculosis
Cited by: 27
Author(s): Olivier Tabone, Raman Verma, Akul Singhania, Probir Chakravarty, William J. Branchett, Christine M. Graham, Jo Lee, Trần Thị Huyền Trang, Frédéric Reynier, Philippe Leissner, Karine Kaiser, Marc Rodrigue, Gerrit Woltmann, Pranabashis Haldar, Anne O’Garra
Software Mentions: 27
Published: about 3 years ago

10.1186/s12859-017-1905-4

ADAGE signature analysis: differential expression analysis with data-defined gene sets
Cited by: 15
Author(s): Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene
Software Mentions: 25
Published: almost 7 years ago

10.1111/joa.13366

Selection on vocal output affects laryngeal morphology in rats
Cited by: 6
Author(s): Raffaela Lesch, Thomas Schwaha, Andrea Orozco, Margaret Shilling, Susan A. Brunelli, Myron A. Hofer, Daniel L. Bowling, Betty Zimmerberg, W. Tecumseh Fitch
Software Mentions: 25
Published: almost 4 years ago

10.3389/fimmu.2021.701085

A Single-Cell Atlas of Lymphocyte Adaptive Immune Repertoires and Transcriptomes Reveals Age-Related Differences in Convalescent COVID-19 Patients
Cited by: 29
Author(s): Florian Bieberich, Rodrigo Vazquez-Lombardi, Alexander Yermanos, Roy Ehling, Derek M Mason, Bastian Wagner, Edo Kapetanovic, Raphaël Brisset Di Roberto, Cédric R. Weber, Miodrag Savic, Fabian Rudolf, Sai T. Reddy
Software Mentions: 23
Published: over 3 years ago

10.7554/eLife.70086

Gaps in global wildlife trade monitoring leave amphibians vulnerable
Cited by: 22
Author(s): Alice C. Hughes, Benjamin Michael Marshall, Colin Thomas Strine
Software Mentions: 23
Published: over 3 years ago

10.1037/rev0000169

Simultaneous consonance in music perception and composition.
Cited by: 47
Author(s): Peter M. C. Harrison, Marcus T. Pearce
Software Mentions: 23
Published: over 4 years ago

10.3390/cells8091045

Systematic Assessment of Blood-Borne MicroRNAs Highlights Molecular Profiles of Endurance Sport and Carbohydrate Uptake
Cited by: 12
Author(s): Fabian Kern, Nicole Ludwig, Christina Backes, Esther Maldener, Tobias Fehlmann, Artur Suleymanov, Eckart Meese, Anne Hecksteden, Andreas Keller, Tim Meyer
Software Mentions: 21
Published: about 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

10.1371/journal.pone.0247002

Chainchecker: An application to visualise and explore transmission chains for Ebola virus disease
Cited by: 2
Author(s): Katy A. M. Gaythorpe, Aaron Morris, Natsuko Imai, Miles Stewart, Jeffrey S. Freeman, Mary J. Choi
Software Mentions: 19
Published: almost 4 years ago

10.3390/cancers13102419

Deep Learning for the Classification of Non-Hodgkin Lymphoma on Histopathological Images
Cited by: 16
Author(s): Georg Steinbuß, Mark Kriegsmann, Christiane Zgorzelski, Alexander Brobeil, Benjamin Goeppert, Sascha Dietrich, Gunhild Mechtersheimer, Katharina Kriegsmann
Software Mentions: 18
Published: over 3 years ago

10.1186/s12859-019-3059-z

HPAanalyze: an R package that facilitates the retrieval and analysis of the Human Protein Atlas data
Cited by: 28
Author(s): Anh Tran, Alex M. Dussaq, Timothy Kennell, Christopher D. Willey, Anita B. Hjelmeland
Software Mentions: 18
Published: about 5 years ago

10.3390/ijms22105385

Deep Learning in Pancreatic Tissue: Identification of Anatomical Structures, Pancreatic Intraepithelial Neoplasia, and Ductal Adenocarcinoma
Cited by: 15
Author(s): Mark Kriegsmann, Katharina Kriegsmann, Georg Steinbuß, Christiane Zgorzelski, Anne Kraft, Matthias M. Gaida
Software Mentions: 18
Published: over 3 years ago

10.1084/jem.20200920

Single-cell analyses identify circulating anti-tumor CD8 T cells and markers for their enrichment
Cited by: 57
Author(s): Kristen E. Pauken, Osmaan Shahid, Kaitlyn A. Lagattuta, Kelly Mahuron, Jacob M. Luber, Margaret M. Lowe, Lüping Huang, Conor P. Delaney, Jaclyn M. Long, Megan E. Fung, Kathleen Newcomer, Katy K. Tsai, Melissa Chow, Samantha Guinn, Juhi R. Kuchroo, Kelly P. Burke, Jason M. Schenkel, Michael D. Rosenblum, Adil Daud, Arlene H. Sharpe, Meromit Singer
Software Mentions: 17
Published: over 3 years ago

10.1001/jamanetworkopen.2020.37227

Trends in US Pediatric Hospital Admissions in 2020 Compared With the Decade Before the COVID-19 Pandemic
Cited by: 115
Author(s): Jonathan Pelletier, Jaskaran Rakkar, Alicia K. Au, Dana Y. Fuhrman, Robert S. B. Clark, Christopher M. Horvat
Software Mentions: 17
Published: almost 4 years ago

10.1371/journal.pone.0219892

Quantification and isolation of Bacillus subtilis spores using cell sorting and automated gating
Cited by: 18
Author(s): Marianna Karava, Felix Bracharz, Johannes Kabisch
Software Mentions: 15
Published: over 5 years ago

10.1371/journal.pone.0223542

Joint emulation of Earth System Model temperature-precipitation realizations with internal variability and space-time and cross-variable correlation: fldgen v2.0 software description
Cited by: 3
Author(s): Abigail Snyder, Robert Link, Kalyn Dorheim, Ben Kravitz, Ben Bond‐Lamberty, Corinne Hartin
Software Mentions: 14
Published: about 5 years ago

10.3390/ijms20174162

SILAC-Based Quantification of TGFBR2-Regulated Protein Expression in Extracellular Vesicles of Microsatellite Unstable Colorectal Cancers
Cited by: 13
Author(s): Fabia Fricke, Malwina Michalak, Uwe Warnken, Ingrid Haußer, Martina Schnölzer, Jürgen Kopitz, Johannes Gebert
Software Mentions: 14
Published: about 5 years ago

10.1038/s41598-020-76843-3

Analyzing long-term impacts of ungulate herbivory on forest-recruitment dynamics at community and species level contrasting tree densities versus maximum heights
Cited by: 10
Author(s): Ursula Nopp‐Mayr, Susanne Reimoser, Friedrich Reimoser, Frederik Sachser, Leopold Obermair, Georg Gratzer
Software Mentions: 14
Published: about 4 years ago

10.2196/mental.9946

Predicting Caller Type From a Mental Health and Well-Being Helpline: Analysis of Call Log Data
Cited by: 9
Author(s): Alexander Grigorash, Siobhan O’Neill, Raymond Bond, Colette Ramsey, Chérie Armour, Maurice Mulvenna
Software Mentions: 13
Published: over 6 years ago

10.1186/s12859-020-03922-7

annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions
Cited by: 3
Author(s): Krutika S. Gaonkar, Fédérico Marini, Komal S. Rathi, Payal Jain, Yuankun Zhu, Nicholas A. Chimicles, Miguel Brown, Ammar S. Naqvi, Bo Zhang, Phillip B. Storm, John M. Maris, Pichai Raman, Adam Resnick, Konstantin Strauch, Jaclyn N. Taroni, Jo Lynne Rokita
Software Mentions: 13
Published: almost 4 years ago

10.12688/f1000research.10742.2

haploR: an R package for querying web-based annotation tools
Cited by: 20
Author(s): Ilya Y. Zhbannikov, Konstantin G. Arbeev, Svetlana V. Ukraintseva, Anatoliy I. Yashin
Software Mentions: 13
Published: over 7 years ago

10.3389/fimmu.2020.620716

Multiscale Modeling of Germinal Center Recapitulates the Temporal Transition From Memory B Cells to Plasma Cells Differentiation as Regulated by Antigen Affinity-Based Tfh Cell Help
Cited by: 14
Author(s): Elena Merino Tejero, Danial Lashgari, Rodrigo García-Valiente, Xuefeng Gao, Fabien Crauste, Philippe A. Robert, Michael Meyer‐Hermann, María Rodríguez Martínez, S. Marieke van Ham, Jeroen E. J. Guikema, Huub Hoefsloot, Antoine H. C. van Kampen
Software Mentions: 13
Published: almost 4 years ago

10.7554/eLife.57116

shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data
Cited by: 35
Author(s): Kenichi Shimada, John A. Bachman, Jeremy Muhlich, Timothy J. Mitchison
Software Mentions: 13
Published: almost 4 years ago

10.1038/s41598-020-73812-8

Synbiotic feed supplementation significantly improves lipid utilization and shows discrete effects on disease resistance in rainbow trout (Oncorhynchus mykiss)
Cited by: 10
Author(s): Kasper Rømer Villumsen, Maki Ohtani, Torunn Forberg, Elisabeth Aasum, John Tinsley, Anders Miki Bojesen
Software Mentions: 12
Published: about 4 years ago

10.26508/lsa.202000770

In vivo CRISPR/Cas9 knockout screen: TCEAL1 silencing enhances docetaxel efficacy in prostate cancer
Cited by: 12
Author(s): Linda Rushworth, Victoria Harle, Peter Repiščák, William Clark, Robin Shaw, Holly Hall, Martin Bushell, Hing Y. Leung, Rachana Patel
Software Mentions: 12
Published: about 4 years ago

10.1111/test.12258

Some teaching resources using R with illustrative examples exploring COVID ‐19 data
Cited by: 0
Author(s): Arthur Berg, Nour Hawila
Software Mentions: 12
Published: over 3 years ago

10.1172/jci.insight.138970

Hypoxia acts as an environmental cue for the human tissue-resident memory T cell differentiation program
Cited by: 21
Author(s): Farah Hasan, Yulun Chiu, Rebecca Shaw, Junmei Wang, Cassian Yee
Software Mentions: 10
Published: over 3 years ago

10.3390/ani10040546

The Welfare Aggregation and Guidance (WAG) Tool: A New Method to Summarize Global Welfare Assessment Data for Equids
Cited by: 11
Author(s): Laura M Kubasiewicz, João B. Rodrigues, Stuart L. Norris, Tamlin Watson, Karen Rickards, Nikki Bell, Andrew Judge, Zoe Raw, Faith Burden
Software Mentions: 9
Published: over 4 years ago

10.1186/s12859-020-3538-2

CIPR: a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments
Cited by: 39
Author(s): H. Atakan Ekiz, Christopher J. Conley, W. Zac Stephens, Ryan M. O’Connell
Software Mentions: 8
Published: over 4 years ago

10.5696/2156-9614-10.27.200912

Levels of PM10 and PM2.5 and Respiratory Health Impacts on School-Going Children in Kenya
Cited by: 8
Author(s): Faridah Hussein Were, Godfrey A. Wafula, Cromwel B Lukorito, Timothy Kamanu
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pgen.1009268

Genetic diversity of the Plasmodium falciparum GTP-cyclohydrolase 1, dihydrofolate reductase and dihydropteroate synthetase genes reveals new insights into sulfadoxine-pyrimethamine antimalarial drug resistance
Cited by: 12
Author(s): Anna Turkiewicz, Emilia Mańko, Colin J. Sutherland, Ernest Diez Benavente, Susana Campino, Taane G. Clark
Software Mentions: 8
Published: almost 4 years ago

10.3390/molecules26123564

Differential Glycosite Profiling—A Versatile Method to Compare Membrane Glycoproteomes
Cited by: 0
Author(s): Malwina Michalak, Martin Simon Kalteis, Aysel Ahadova, Matthias Kloor, Mark Kriegsmann, Katharina Kriegsmann, Uwe Warnken, Dominic Helm, Jürgen Kopitz
Software Mentions: 8
Published: over 3 years ago

10.1093/bioinformatics/bty088

SecretSanta: flexible pipelines for functional secretome prediction
Cited by: 10
Author(s): Anna Gogleva, Hajk-Georg Drost, Sebastián Schornack
Software Mentions: 7
Published: almost 7 years ago

10.3390/ijms22189979

A Novel UPLC-MS/MS Method Identifies Organ-Specific Dipeptide Profiles
Cited by: 5
Author(s): Elena Heidenreich, Tilman Pfeffer, Tamara Kracke, Nils Mechtel, Peter P. Nawroth, Georg F. Hoffmann, Claus Peter Schmitt, Rüdiger Hell, Gernot Poschet, Verena Peters
Software Mentions: 7
Published: about 3 years ago

10.1590/0074-02760190105

Gene regulatory network inference and analysis of multidrug-resistant Pseudomonas aeruginosa
Cited by: 5
Author(s): Fernando Medeiros Filho, Ana Paula Barbosa do Nascimento, M. Tadeu dos Santos, Ana Paula D’Alincourt Carvalho-Assef, Fabrício Silva
Software Mentions: 7
Published: almost 6 years ago

10.12688/f1000research.25141.1

CRI iAtlas: an interactive portal for immuno-oncology research
Cited by: 33
Author(s): James A. Eddy, Vésteinn Thórsson, Andrew Lamb, David L. Gibbs, Carolina Heimann, Jia Yu, Verena Chung, Yooree Chae, Kristen K. Dang, Benjamin G. Vincent, Ilya Shmulevich, Justin Guinney
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pone.0249573

Challenges during the execution, results, and monitoring phases of ecological restoration: Learning from a country-wide assessment
Cited by: 11
Author(s): Moisés Méndez‐Toribio, Cristina Martínez‐Garza, Eliane Ceccon
Software Mentions: 5
Published: over 3 years ago

10.3389/fcimb.2021.715998

Co-Occurrence of Viruses, Plant Pathogens, and Symbionts in an Underexplored Hemipteran Clade
Cited by: 0
Author(s): McKinlee M. Salazar, Mônica Tallarico Pupo, Amanda M. V. Brown
Software Mentions: 4
Published: about 3 years ago

10.3389/fonc.2021.683282

Development of Nomograms for Predicting Lymph Node Metastasis and Distant Metastasis in Newly Diagnosed T1-2 Non-Small Cell Lung Cancer: A Population-Based Analysis
Cited by: 7
Author(s): Yihong Qi, Shuangshuang Wu, Linghui Tao, Yunfu Shi, Wenjuan Yang, Lina Zhou, Bo Zhang, Jing Li
Software Mentions: 4
Published: about 3 years ago

10.1038/s41598-019-48283-1

De novo transcriptome assembly for four species of crustose coralline algae and analysis of unique orthologous genes
Cited by: 9
Author(s): Tessa M. Page, Carmel McDougall, Guillermo Díaz-Pulido
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-020-03601-7

AutoCloner: automatic homologue-specific primer design for full-gene cloning in polyploids
Cited by: 0
Author(s): Alexander Coulton, Keith J. Edwards
Software Mentions: 4
Published: over 4 years ago

10.3390/antibiotics9120918

Global Trends in Antimicrobial Use in Food Animals from 2017 to 2030
Cited by: 233
Author(s): Katie Tiseo, Laura Huber, Marius Gilbert, Timothy P. Robinson, Thomas P. Van Boeckel
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41420-021-00486-0

Hyperbaric oxygen promotes not only glioblastoma proliferation but also chemosensitization by inhibiting HIF1α/HIF2α-Sox2
Cited by: 5
Author(s): Pan Wang, Shipeng Gong, Jinyu Pan, Junwei Wang, Dewei Zou, Shuanglong Xiong, Lu Zhao, Yan Qian, Yangming Deng, Bin Liao
Software Mentions: 2
Published: over 3 years ago

10.1038/s41419-021-03598-8

HIF1α/HIF2α–Sox2/Klf4 promotes the malignant progression of glioblastoma via the EGFR–PI3K/AKT signalling pathway with positive feedback under hypoxia
Cited by: 23
Author(s): Pan Wang, Lu Zhao, Shipeng Gong, Shuanglong Xiong, Junwei Wang, Dewei Zou, Jinyu Pan, Yangmin Deng, Yan Qian, Bin Liao
Software Mentions: 2
Published: over 3 years ago

Projects: cran: tibble

Papers Mentioning tibble 47