Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: d3
https://packages.ecosyste.ms/registries/pypi.org/packages/d3
A D3.js programming API for python
1 version
Latest release: almost 8 years ago
122 downloads last month
Papers Mentioning d3 22
10.1186/s13104-017-2607-8
NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networksCited by: 28
Author(s): Θεοδόσιος Θεοδοσίου, Georgios Efstathiou, Nikolas Papanikolaou, Nikos C. Kyrpides, Pantelis G. Bagos, Ioannis Iliopoulos, Georgios A. Pavlopoulos
Software Mentions: 11
Published: about 7 years ago
10.1093/bioinformatics/btu616
Shiny-phyloseq: Web application for interactive microbiome analysis with provenance trackingCited by: 112
Author(s): Paul J. McMurdie, Susan Holmes
Software Mentions: 7
Published: almost 10 years ago
10.3762/bjnano.6.165
The eNanoMapper database for nanomaterial safety informationCited by: 82
Author(s): Nina Jeliazkova, Charalampos Chomenidis, Philip Doganis, Bengt Fadeel, Roland C. Grafström, Barry Hardy, Janna Hastings, Markus Hegi, Vedrin Jeliazkov, Nikolay Kochev, Pekka Kohonen, Cristian R. Munteanu, Haralambos Sarimveis, Bart Smeets, Pantelis Sopasakis, Georgia Tsiliki, David Vorgrimmler, Egon Willighagen
Software Mentions: 7
Published: about 9 years ago
10.1186/s12859-020-03917-4
ped_draw: pedigree drawing with easeCited by: 2
Author(s): Matt Velinder, Dillon Lee, Gábor Marth
Software Mentions: 5
Published: almost 4 years ago
10.1098/rstb.2014.0240
Assigning and visualizing germline genes in antibody repertoiresCited by: 19
Author(s): Simon D. W. Frost, Ben Murrell, Alamgir Hossain, Gregg J. Silverman, Sergei L. Kosakovsky Pond
Software Mentions: 5
Published: about 9 years ago
10.1371/journal.pone.0111928
CollaborationViz: Interactive Visual Exploration of Biomedical Research Collaboration NetworksCited by: 12
Author(s): Jiang Bian, Mengjun Xie, Teresa J. Hudson, Hari Eswaran, Mathias Brochhausen, Josh Hanna, William R. Hogan
Software Mentions: 3
Published: almost 10 years ago
10.1038/s41598-021-94959-y
Fast and accurate exhaustive higher-order epistasis search with BitEpiCited by: 8
Author(s): Arash Bayat, Brendan Hosking, Yatish Jain, Cameron Hosking, Milindi Kodikara, Daniel Reti, Natalie A. Twine, Denis C. Bauer
Software Mentions: 3
Published: about 3 years ago
10.1371/journal.pone.0084860
STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the CloudCited by: 26
Author(s): Konrad J. Karczewski, Guy Haskin Fernald, Martin Ar, M Snyder, Nicholas P. Tatonetti, Joel T. Dudley
Software Mentions: 3
Published: over 10 years ago
10.1038/s41598-018-37411-y
INSIdE NANO: a systems biology framework to contextualize the mechanism-of-action of engineered nanomaterialsCited by: 25
Author(s): Angela Serra, Ivica Letunić, Vittorio Fortino, Richard D. Handy, Bengt Fadeel, Roberto Tagliaferri, Dario Greco
Software Mentions: 3
Published: over 5 years ago
10.1186/s12870-020-02659-y
Database: web application for visualization of the cumulated RNAseq data against the salicylic acid (SA) and methyl jasmonate (MeJA) treatment of Arabidopsis thalianaCited by: 2
Author(s): Dong U Woo, Ho Hwi Jeon, Halim Park, Jin Hwa Park, Yejin Lee, Yang-Jae Kang
Software Mentions: 3
Published: almost 4 years ago
10.1534/g3.120.401775
BioLitMine: Advanced Mining of Biomedical and Biological Literature About Human Genes and Genes from Major Model OrganismsCited by: 7
Author(s): Yanhui Hu, Verena Chung, Aram Comjean, Jonathan Rodiger, Fnu Nipun, Norbert Perrimon, Stephanie E. Mohr
Software Mentions: 3
Published: almost 4 years ago
10.1038/sdata.2015.75
Pantheon 1.0, a manually verified dataset of globally famous biographiesCited by: 40
Author(s): Amy Z. Yu, Shahar Ronen, Kevin Hu, Tiffany Lu, César A. Hidalgo
Software Mentions: 3
Published: over 8 years ago
10.2196/19367
Complex Reporting of the COVID-19 Epidemic in the Czech Republic: Use of an Interactive Web-Based App in PracticeCited by: 50
Author(s): Martin Komenda, Vojtěch Bulhart, Matěj Karolyi, Jiří Jarkovský, Jan Mužı́k, Ondřej Májek, Lenka Šnajdrová, Petra Růžičková, Jarmila Rážová, Roman Prymula, Barbora Macková, P Brezovský, Jan Marounek, V. Černý, Ladislav Dušek
Software Mentions: 2
Published: over 4 years ago
10.1186/s12859-017-1706-9
dictyExpress: a web-based platform for sequence data management and analytics in Dictyostelium and beyondCited by: 24
Author(s): Miha Štajdohar, Rafael D. Rosengarten, Janez Kokošar, Luka Jeran, Domen Blenkus, Gad Shaulsky, Blaž Zupan
Software Mentions: 2
Published: over 7 years ago
10.1093/bioinformatics/btt159
Biographer: web-based editing and rendering of SBGN compliant biochemical networksCited by: 14
Author(s): Falko Krause, Marvin Schulz, Ben Ripkens, Max Flöttmann, Marcus Krantz, Edda Klipp, Thomas Handorf
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0231826
Advancing clinical cohort selection with genomics analysis on a distributed platformCited by: 1
Author(s): Jaclyn Smith, Melvin Lathara, Hollis Wright, Brian Hill, Nalini Ganapati, Ganapati Srinivasa, Christopher T. Denny
Software Mentions: 2
Published: over 4 years ago
10.1093/database/bav045
MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouseCited by: 15
Author(s): Hong Dong Li, Gilbert S. Omenn, Yuanfang Guan
Software Mentions: 2
Published: over 9 years ago
10.1534/g3.119.400908
BlobToolKit – Interactive Quality Assessment of Genome AssembliesCited by: 644
Author(s): Richard Challis, E. G. Richards, Jeena Rajan, Guy Cochrane, Mark Blaxter
Software Mentions: 2
Published: over 4 years ago
10.1038/s41598-019-57038-x
SWAV: a web-based visualization browser for sliding window analysisCited by: 8
Author(s): Zhenglin Zhu, Yawang Wang, Xichuan Zhou, Liuqing Yang, Geng Meng, Ze Zhang
Software Mentions: 2
Published: over 4 years ago
10.1186/s12859-016-1062-1
QUADrATiC: scalable gene expression connectivity mapping for repurposing FDA-approved therapeuticsCited by: 22
Author(s): Paul G. O’Reilly, Qing Wen, Peter Bankhead, Philip D. Dunne, Darragh G. McArt, Suzanne McPherson, Peter Hamilton, Ken I. Mills, Shudong Zhang
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0219531
Metabolic features of Gulf War illnessCited by: 25
Author(s): Robert K. Naviaux, Jane C. Naviaux, Kefeng Li, Lin Wang, Jonathan M. Monk, A. Taylor Bright, Hayley J. Koslik, Janis B. Ritchie, Beatrice A. Golomb
Software Mentions: 1
Published: about 5 years ago
10.1186/s12859-019-2642-7
Statistical assessment and visualization of synergies for large-scale sparse drug combination datasetsCited by: 23
Author(s): Arnaud Amzallag, Sridhar Ramaswamy, Cyril H. Benes
Software Mentions: 1
Published: over 5 years ago