pypi: docker | Projects | Ecosyste.ms: Papers

10.1186/s12859-021-04142-3

SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses
Cited by: 11
Author(s): Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise A Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordóñez, Andrew E. Jaffe, Leonardo Collado‐Torres
Software Mentions: 13
Published: over 3 years ago

10.1371/journal.pcbi.1008316

Ten simple rules for writing Dockerfiles for reproducible data science
Cited by: 36
Author(s): Daniel Nüst, Vanessa Sochat, Ben Marwick, Stephen J. Eglen, T. Head, Tony Hirst, Benjamin D. Evans
Software Mentions: 11
Published: almost 4 years ago

10.1186/s12859-018-2296-x

Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines
Cited by: 47
Author(s): Neha Kulkarni, Luca Alessandrì, Riccardo Panero, Maddalena Arigoni, Martina Olivero, Giulio Ferrero, Francesca Cordero, Marco Beccuti, Raffaele Calogero
Software Mentions: 10
Published: about 6 years ago

10.1093/gigascience/giz149

Refgenie: a reference genome resource manager
Cited by: 28
Author(s): Michał Stolarczyk, Vincent Reuter, Jason P. Smith, Neal E. Magee, Nathan C. Sheffield
Software Mentions: 9
Published: almost 5 years ago

10.3389/fmicb.2021.649517

Decentralized Investigation of Bacterial Outbreaks Based on Hashed cgMLST
Cited by: 15
Author(s): Carlus Deneke, Laura Uelze, Holger Brendebach, Simon H. Tausch, Burkhard Malorny
Software Mentions: 9
Published: over 3 years ago

10.1093/gigascience/giz147

Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa
Cited by: 16
Author(s): Miriam Payá‐Milans, Laura Poza‐Viejo, Patxi San Martín-Úriz, David Lara‐Astiaso, Mark D. Wilkinson, Pedro Crevillén
Software Mentions: 8
Published: almost 5 years ago

10.3390/ijms21010293

Docker4Circ: A Framework for the Reproducible Characterization of circRNAs from RNA-Seq Data
Cited by: 8
Author(s): Giulio Ferrero, Nicola Licheri, Lucia Coscujuela Tarrero, Carlo De Intinis, Valentina Miano, Raffaele Calogero, Francesca Cordero, Michele De Bortoli, Marco Beccuti
Software Mentions: 8
Published: almost 5 years ago

10.7554/eLife.14334

TissueMiner: A multiscale analysis toolkit to quantify how cellular processes create tissue dynamics
Cited by: 104
Author(s): Raphaël Etournay, Matthias Merkel, Marko Popović, Holger Brandl, Natalie A. Dye, Benoît Aigouy, Guillaume Salbreux, Suzanne Eaton, Frank Jülicher
Software Mentions: 7
Published: over 8 years ago

10.7717/peerj.5853

BioInstaller: a comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform
Cited by: 3
Author(s): Jianfeng Li, Bowen Cui, Yuting Dai, Lijun Bai, Huang Jy
Software Mentions: 7
Published: about 6 years ago

10.1186/s12859-020-03648-6

A computational framework for modeling and studying pertussis epidemiology and vaccination
Cited by: 4
Author(s): Paolo Castagno, Simone Pernice, Gianni Ghetti, Massimiliano Povero, Lorenzo Pradelli, Daniela Paolotti, Gianfranco Balbo, Matteo Sereno, Marco Beccuti
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pcbi.1005209

BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods
Cited by: 203
Author(s): Krzysztof J. Gorgolewski, Fidel Alfaro-Almagro, Tibor Auer, Pierre Bellec, Mihai Capotă, M. Mallar Chakravarty, Nathan W. Churchill, Alexander L. Cohen, R. Cameron Craddock, Gabriel A. Devenyi, Anders Eklund, Oscar Estéban, Guillaume Flandin, Samik Ghosh, J. Swaroop Guntupalli, Mark Jenkinson, Anisha Keshavan, Gregory Kiar, Franziskus Liem, Pradeep Reddy Raamana, David Raffelt, Christopher J. Steele, Pierre-Olivier Quirion, Robert E. Smith, Stephen C. Strother, Gaël Varoquaux, Yida Wang, Tal Yarkoni, Russell A. Poldrack
Software Mentions: 5
Published: over 7 years ago

10.3389/fdata.2020.00022

The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons
Cited by: 22
Author(s): Scott Christley, Ademar Aguiar, George Blanck, Felix Breden, Syed Ahmad Chan Bukhari, Christian E. Busse, Jerome Jaglale, Srilakshmy L. Harikrishnan, Uri Laserson, Bjoern Peters, Artur Rocha, Chaim A. Schramm, Sarah E. Taylor, Jason A. Vander Heiden, Bojan Zimonja, Corey T. Watson, Brian Corrie, Lindsay G. Cowell
Software Mentions: 4
Published: over 4 years ago

10.1186/s12859-017-1663-3

“gnparser”: a powerful parser for scientific names based on Parsing Expression Grammar
Cited by: 10
Author(s): Dmitry Mozzherin, Alexander A. Myltsev, David J. Patterson
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0177459

Singularity: Scientific containers for mobility of compute
Cited by: 895
Author(s): Gregory M. Kurtzer, Vanessa Sochat, Michael Bauer
Software Mentions: 4
Published: over 7 years ago

10.1093/database/bax039

GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species
Cited by: 14
Author(s): Richard Challis, Sujai Kumar, Lewis Stevens, Mark Blaxter
Software Mentions: 4
Published: almost 8 years ago

10.3389/fendo.2021.714561

Biased Coupling to β-Arrestin of Two Common Variants of the CB2 Cannabinoid Receptor
Cited by: 9
Author(s): Gábor Turu, Eszter Soltész‐Katona, András Tóth, C.C. Juhasz, Miklós Cserző, Ádám Misák, András Balla, Marc G. Caron, László Hunyady
Software Mentions: 4
Published: about 3 years ago

10.3390/s21030772

Multi-Layer Blockchain-Based Security Architecture for Internet of Things
Cited by: 58
Author(s): Houshyar Honar Pajooh, M. A. Rashid, Fakhrul Alam, Serge Demidenko
Software Mentions: 4
Published: almost 4 years ago

10.3390/s18124226

Design Methodology of Microservices to Support Predictive Analytics for IoT Applications
Cited by: 25
Author(s): Sajjad Ali, Muhammad Aslam Jarwar, Ilyoung Chong
Software Mentions: 3
Published: almost 6 years ago

10.3389/fchem.2020.00046

ChEMBL-Likeness Score and Database GDBChEMBL
Cited by: 29
Author(s): Sven Bühlmann, Jean‐Louis Reymond
Software Mentions: 3
Published: almost 5 years ago

10.1016/j.xpro.2021.100505

Computational generation of proteins with predetermined three-dimensional shapes using ProteinSolver
Cited by: 6
Author(s): Alexey Strokach, David Becerra, Carles Corbi‐Verge, Albert Perez-Riba, Philip M. Kim
Software Mentions: 3
Published: over 3 years ago

10.1093/gigascience/giab001

metaXplor: an interactive viral and microbial metagenomic data manager
Cited by: 2
Author(s): Guilhem Sempéré, Adrien Pétel, Magsen Abbé, Pierre Lefeuvre, Philippe Roumagnac, Frédéric Mahé, Gaël Baurens
Software Mentions: 3
Published: almost 4 years ago

10.1007/s43926-021-00008-5

End-to-end experimentation of a 5G vertical within the scope of blended learning
Cited by: 12
Author(s): Ngombo Armando, Rui M. Almeida, José Marcelo Fernandes, Jorge Sá Silva, Fernando Boavida
Software Mentions: 3
Published: over 3 years ago

10.3390/s20164393

A Model for the Remote Deployment, Update, and Safe Recovery for Commercial Sensor-Based IoT Systems
Cited by: 1
Author(s): Alexandru Radovici, Ioana Culic, Daniel E. Rosner, Flavia Oprea
Software Mentions: 3
Published: over 4 years ago

10.3390/s19214798

MicroServices Suite for Smart City Applications
Cited by: 23
Author(s): Claudio Badii, Pierfrancesco Bellini, Angelo Difino, Paolo Nesi, Gianni Pantaleo, Michela Paolucci
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-020-6568-2

GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
Cited by: 48
Author(s): Nancy Manchanda, John L. Portwood, Margaret R. Woodhouse, Arun S. Seetharam, Carolyn J. Lawrence‐Dill, Carson M. Andorf, Matthew B. Hufford
Software Mentions: 3
Published: over 4 years ago

10.3390/e23070914

Leadership Hijacking in Docker Swarm and Its Consequences
Cited by: 4
Author(s): Adi Farshteindiker, Rami Puzis
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-018-2295-y

BITS 2017: the annual meeting of the Italian Society of Bioinformatics
Cited by: 0
Author(s): Giuliano Armano, Giorgio Fotia, Andrea Manconi
Software Mentions: 2
Published: about 6 years ago

10.1186/s13742-015-0073-6

Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant
Cited by: 65
Author(s): Andreas Bremges, Irena Maus, Peter Belmann, Felix Gregor Eikmeyer, Anderson M. Winkler, Andreas Albersmeier, Alfred Pühler, Andreas Schlüter, Alexander Sczyrba
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pcbi.1008194

Discovering functional sequences with RELICS, an analysis method for CRISPR screens
Cited by: 5
Author(s): Patrick C. Fiaux, Hsiuyi V. Chen, Poshen B. Chen, Aaron R Chen, Graham McVicker
Software Mentions: 2
Published: about 4 years ago

10.1186/s12967-020-02675-4

Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants
Cited by: 12
Author(s): Alice Massacci, Eleonora Sperandio, Lorenzo D’Ambrosio, Mariano Maffei, Fabio Palombo, Luigi Aurisicchio, Gennaro Ciliberto, Matteo Pallocca
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-017-06453-z

Identification of a Flavonoid Glucosyltransferase Involved in 7-OH Site Glycosylation in Tea plants (Camellia sinensis)
Cited by: 34
Author(s): Xinlong Dai, Juhua Zhuang, Ying-Ling Wu, Peiqiang Wang, Guifu Zhao, Yajun Li, Xiaolan Jiang, Liping Gao, Tao Xia
Software Mentions: 1
Published: over 7 years ago

10.1186/s13742-015-0080-7

NCBI BLAST+ integrated into Galaxy
Cited by: 164
Author(s): Peter J. A. Cock, John Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo
Software Mentions: 1
Published: about 9 years ago

10.3389/fphar.2018.00127

Tricaproin Isolated From Simarouba glauca Inhibits the Growth of Human Colorectal Carcinoma Cell Lines by Targeting Class-1 Histone Deacetylases
Cited by: 18
Author(s): Asha Jose, Motamarri Venkata Naga Lalitha Chaitanya, K Elango, SubbaRao V. Madhunapantula
Software Mentions: 1
Published: over 6 years ago

10.3390/s20113268

Implementation of High-Performance Blockchain Network Based on Cross-Chain Technology for IoT Applications
Cited by: 17
Author(s): Ting‐Hui Lin, Xu Yang, Taoyi Wang, Peng Tu, Feng Xu, Shengxiong Lao, Siyuan Ma, Hanfeng Wang, Hao Wen-jiang
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0221858

Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies
Cited by: 3
Author(s): Giltae Song, Jongin Lee, Ju‐Yeon Kim, Seok-Woo Kang, Ho-Yong Lee, Daehong Kwon, Daehwan Lee, Gregory I. Lang, J. Michael Cherry, Jaebum Kim
Software Mentions: 1
Published: about 5 years ago

10.12688/f1000research.8935.1

Bringing your tools to CyVerse Discovery Environment using Docker
Cited by: 25
Author(s): Upendra Kumar Devisetty, Kathleen Kennedy, Paul Sarando, Nirav Merchant, Eric Lyons
Software Mentions: 1
Published: over 8 years ago

10.1093/database/baz077

Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases
Cited by: 21
Author(s): Shawna Spoor, Cuixia Cheng, Lacey-Anne Sanderson, Bradford Condon, Abdullah Almsaeed, Ming Chen, Anthony Bretaudeau, Helena Rasche, Sook Jung, Dorrie Main, Kirstin E. Bett, Margaret Staton, Jill L. Wegrzyn, F. Alex Feltus, Stephen P. Ficklin
Software Mentions: 1
Published: almost 6 years ago

10.12688/f1000research.20590.2

Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat maps
Cited by: 26
Author(s): Michaël Ryan, Mark Stucky, Chris Wakefield, James Melott, Rehan Akbani, John N. Weinstein, Bradley M. Broom
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-020-06875-6

MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data
Cited by: 4
Author(s): Chi-Ming Leung, Dinghua Li, Xin Yan, Wai-Chun Law, Yifan Zhang, Hing-Fung Ting, Ruibang Luo, Tak-Wah Lam
Software Mentions: 1
Published: almost 4 years ago

Projects: pypi: docker

Papers Mentioning docker 39