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: pip

https://packages.ecosyste.ms/registries/pypi.org/packages/pip

The PyPA recommended tool for installing Python packages.
136 versions
Latest release: 11 months ago
789 dependent packages
204,709,421 downloads last month

Papers Mentioning pip 21

The role of metadata in reproducible computational research
Cited by: 38
Author(s): Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Karthik Ram, Jane Greenberg
Software Mentions: 21
Published: about 3 years ago

10.1093/bioinformatics/bty149

NanoPack: visualizing and processing long-read sequencing data
Cited by: 1,423
Author(s): Wouter De Coster, Svenn D’Hert, Darrin T. Schultz, Marc Cruts, Christine Van Broeckhoven
Software Mentions: 18
Published: over 6 years ago

10.12688/f1000research.15140.2

Recommendations for the packaging and containerizing of bioinformatics software
Cited by: 32
Author(s): Bjoern Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes L. Röst, Timo Sachsenberg, Brian D. O’Connor, Fábio Madeira, Victoria Domínguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C. Jiménez, BioContainers Community, Yasset Perez‐Riverol
Software Mentions: 14
Published: over 5 years ago

10.1186/s40679-016-0031-0

Analyzing microtomography data with Python and the scikit-image library
Cited by: 22
Author(s): Emmanuelle Gouillart, Juan Nunez-Iglesias, Stéfan van der Walt
Software Mentions: 14
Published: almost 8 years ago

10.1186/s13321-020-00455-2

spyrmsd: symmetry-corrected RMSD calculations in Python
Cited by: 23
Author(s): Rocco Meli, Philip C. Biggin
Software Mentions: 13
Published: about 4 years ago

10.1016/j.cmpb.2018.01.025

NiftyNet: a deep-learning platform for medical imaging
Cited by: 429
Author(s): Eli Gibson, Wenqi Li, Carole H. Sudre, Lucas Fidon, Dzhoshkun I. Shakir, Guotai Wang, Zach Eaton-Rosen, Robert Gray, Tom Doel, Yipeng Hu, T. Whyntie, Parashkev Nachev, Marc Modat, Dean C. Barratt, Sébastien Ourselin, M. Jorge Cardoso, Tom Vercauteren
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.pbio.3001365

PhyloFisher: A phylogenomic package for resolving eukaryotic relationships
Cited by: 34
Author(s): Alexander K. Tice, David Žihala, Tomáš Pánek, Robert E. Jones, Eric D. Salomaki, Serafim Nenarokov, Fabien Burki, Marek Eliáš, Laura Eme, Andrew J. Roger, Antonis Rokas, Xing‐Xing Shen, Jürgen F. H. Strassert, Martin Kolísko, Matthew W. Brown
Software Mentions: 9
Published: about 3 years ago

10.3390/s20051500

Towards IoT-Aided Human–Robot Interaction Using NEP and ROS: A Platform-Independent, Accessible and Distributed Approach
Cited by: 15
Author(s): Enrique Coronado, Gentiane Venture
Software Mentions: 9
Published: over 4 years ago

10.3390/e23060657

Variational Quantum Chemistry Programs in JaqalPaq
Cited by: 2
Author(s): Oliver G. Maupin, Andrew David Baczewski, Peter J. Love, Andrew J. Landahl
Software Mentions: 7
Published: over 3 years ago

10.12688/f1000research.15830.2

An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data
Cited by: 2
Author(s): Clarence K. Mah, Alexander T. Wenzel, Edwin F. Juarez, Thorin Tabor, Michael Reich, Jill P. Mesirov
Software Mentions: 7
Published: over 5 years ago

10.1523/ENEURO.0085-20.2020

<i>neurotic</i>: Neuroscience Tool for Interactive Characterization
Cited by: 4
Author(s): Jeffrey P. Gill, Samuel Garcia, Lena H. Ting, Mengnan Wu, Hillel J. Chiel
Software Mentions: 6
Published: over 4 years ago

10.3390/vision3040055

Development of Open-source Software and Gaze Data Repositories for Performance Evaluation of Eye Tracking Systems
Cited by: 0
Author(s): Anuradha Kar, Peter Corcoran
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pone.0210347

EMBL2checklists: A Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA
Cited by: 6
Author(s): Michael Gruenstaeudl, Yannick Hartmaring
Software Mentions: 5
Published: over 5 years ago

10.3390/v12121424

NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index
Cited by: 3
Author(s): Joan Martí-Carreras, Alejandro Rafael Gener, Sierra Miller, Anderson F. Brito, Christiam Camacho, Ryan Connor, Ward Deboutte, Cody Glickman, David M. Kristensen, Wynn K. Meyer, Sejal Modha, Alexis L. Norris, Surya Saha, Anna K. Belford, Evan Biederstedt, J. Rodney Brister, Jan P. Buchmann, Nicholas P. Cooley, Robert A. Edwards, Kiran Javkar, Michael Muchow, Harihara Subrahmaniam Muralidharan, Charles Pepe-Ranney, Nidhi Shah, Migun Shakya, Michael J. Tisza, Benjamin J. Tully, Bert Vanmechelen, Valerie Christine Virta, Jake L. Weissman, Vadim Zalunin, Alexandre Efremov, Ben Busby
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pcbi.1006384

Context-explorer: Analysis of spatially organized protein expression in high-throughput screens
Cited by: 9
Author(s): Joel Östblom, Emanuel Joseph Paul Nazareth, Mukul Tewary
Software Mentions: 5
Published: over 5 years ago

10.3389/fninf.2021.614881

MIIND : A Model-Agnostic Simulator of Neural Populations
Cited by: 4
Author(s): Hugh Osborne, Yi Ming Lai, Mikkel Elle Lepperød, David Sichau, Lukas Deutz, Marc de Kamps
Software Mentions: 5
Published: about 3 years ago

10.12688/f1000research.20233.1

A Sequence Distance Graph framework for genome assembly and analysis
Cited by: 3
Author(s): Luis Yanes, Gonzalo Garcia Accinelli, Jonathan Wright, Ben J. Ward, Bernardo Clavijo
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pcbi.1007007

Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks
Cited by: 74
Author(s): Adam Rule, Amanda Birmingham, Cristal Zuñiga, Ilkay Altıntaş, Shih-Cheng Huang, Rob Knight, Niema Moshiri, Manh Duc Nguyen, Sara Brin Rosenthal, Fernando Pérez, Peter W. Rose
Software Mentions: 3
Published: about 5 years ago

10.1093/gigascience/giz054

Software engineering for scientific big data analysis
Cited by: 19
Author(s): Björn Grüning, Samuel Lampa, Marc Vaudel, Daniel Blankenberg
Software Mentions: 2
Published: over 5 years ago

10.1107/S205979832000056X

<i>ALIXE</i>: a phase-combination tool for fragment-based molecular replacement
Cited by: 14
Author(s): Claudia Millán, Elisabet Jiménez, Antonia Schuster, Kay Diederichs, Isabel Usón
Software Mentions: 2
Published: over 4 years ago

10.1093/bioinformatics/btz278

ORCA: a comprehensive bioinformatics container environment for education and research
Cited by: 10
Author(s): Shaun D. Jackman, Tatyana Mozgacheva, Susie Chen, Brendan O’Huiginn, Lance R. Bailey, İnanç Birol, Steven J.M. Jones
Software Mentions: 1
Published: over 5 years ago