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: bioconductor: clipper
https://packages.ecosyste.ms/registries/bioconductor.org/packages/clipper
Gene Set Analysis Exploiting Pathway Topology
1 version
Latest release: about 1 year ago
1 dependent package
28,711 downloads total
Papers Mentioning clipper 8
10.3390/metabo9100200
The metaRbolomics Toolbox in Bioconductor and beyondCited by: 61
Author(s): Jan Stanstrup, Corey D. Broeckling, Rick Helmus, Nils Hoffmann, Ewy A. Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Michael Rainer, Reza M. Salek, Tobias Schulze, Emma L. Schymanski, Michael A. Stravs, Etienne Thévenot, Hendrik Treutler, Ralf Weber, Egon Willighagen, Michael Witting, Steffen Neumann
Software Mentions: 92
Published: about 5 years ago
10.3390/biology3010085
R-Based Software for the Integration of Pathway Data into Bioinformatic AlgorithmsCited by: 17
Author(s): Frank Krämer, Michaela Bayerlová, Tim Beißbarth
Software Mentions: 28
Published: over 10 years ago
10.1186/s12859-015-0763-1
ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq dataCited by: 29
Author(s): Ivana Ihnatová, Eva Budínská
Software Mentions: 12
Published: about 9 years ago
10.1002/pro.3299
Automating tasks in protein structure determination with the clipper python moduleCited by: 6
Author(s): Stuart McNicholas, Tristan I. Croll, Tom Burnley, Colin M. Palmer, Soon Wen Hoh, Huw T. Jenkins, E.J. Dodson, Kevin Cowtan, Jon Agirre
Software Mentions: 10
Published: almost 7 years ago
10.1107/S2059798317007859
Recent developments in the<i>CCP-EM</i>software suiteCited by: 266
Author(s): Tom Burnley, Colin M. Palmer, Martyn Winn
Software Mentions: 7
Published: over 7 years ago
10.18632/oncotarget.14107
High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomesCited by: 59
Author(s): Marta R. Hidalgo, Cankut Çubuk, Alicia Amadoz, Francisco Salavert, José Carbonell-Caballero, Joaquín Dopazo
Software Mentions: 5
Published: almost 8 years ago
10.1053/j.gastro.2020.09.043
Targeting DNA Damage Response and Replication Stress in Pancreatic CancerCited by: 73
Author(s): Stephan Dreyer, Rosanna Upstill-Goddard, Viola Paulus-Hock, Clara Paris, Eirini-Maria Lampraki, Eloïse Dray, Bryan Serrels, Giuseppina Caligiuri, Selma Rebus, Dennis Plenker, Zachary Galluzzo, Holly Brunton, Richard Cunningham, Mathias Tesson, Craig Nourse, Ulla-Maja Bailey, Marc D. Jones, Kim Moran-Jones, Derek W. Wright, Fraser Duthie, Karin A. Oien, Lisa Evers, Colin McKay, Grant A. McGregor, Aditi Gulati, Rachel Brough, Ilirjana Bajrami, Stephen J. Pettitt, Michele L. Dziubinski, Juliana Candido, Frances R. Balkwill, Simon T. Barry, Robert Grützmann, Lola Rahib, Amber Johns, Marina Pajic, Fieke E. M. Froeling, Philip Beer, Elizabeth A. Musgrove, Gloria M. Petersen, Alan Ashworth, Margaret C. Frame, Howard C. Crawford, Diane M. Simeone, Chris Lord, Debabrata Mukhopadhyay, Christian Pilarsky, David A. Tuveson, Susanna L. Cooke, Nigel B. Jamieson, Jennifer P. Morton, Owen J. Sansom, Peter J. Bailey, Andrew V. Biankin, David K. Chang, Sarah E. Allison, Peter J. Bailey, Ulla-Maja Bailey, Andrew V. Biankin, Dario Beraldi, Holly Brunton, Giuseppina Caligiuri, Euan Cameron, David K. Chang, Susanna L. Cooke, Richard Cunningham, Stephan Dreyer, Paul Grimwood, Shane Kelly, Eirini-Maria Lampraki, John L. Marshall, Sancha Martin, Brian McDade, Daniel L. McElroy, Elizabeth A. Musgrove, Craig Nourse, Viola Paulus-Hock, Donna T. Ramsay, Rosanna Upstill-Goddard, Derek W. Wright, Marc D. Jones, Lisa Evers, Selma Rebus, Lola Rahib, Bryan Serrels, Jane Hair, Nigel B. Jamieson, Colin McKay, Paul Westwood, Nicola Williams, Fraser Duthie, Andrew V. Biankin, Amber Johns, Amanda Mawson, David K. Chang, Christopher J. Scarlett, Mary-Anne L. Brancato, Sarah J. Rowe, Skye Simpson, Mona Martyn-Smith, Michelle T. Thomas, Lorraine A. Chantrill, Venessa T. Chin, Angela Chou, Mark J. Cowley, Jeremy L. Humphris, Marc D. Jones, R. Scott Mead, Adnan Nagrial, Marina Pajic, Jessica Pettit, Mark Pinese, Ilse Rooman, Jianmin Wu, Tao Jiang, Renee DiPietro, Clare Watson, Angela Steinmann, Hong Ching Lee, Rachel Wong, Andreia V. Pinho, Marc Giry-Laterrière, Roger J. Daly, Elizabeth A. Musgrove, Robert L. Sutherland, Sean M. Grimmond, Nicola Waddell, Karin S. Kassahn, David Miller, Peter J. Wilson, Ann‐Marie Patch, Sarah Song, Ivon Harliwong, Senel Idrisoglu, Craig Nourse, Ehsan Nourbakhsh, Suzanne Manning, Shivangi Wani, Milena Gongora, Matthew Anderson, Oliver Holmes, Conrad Leonard, Darrin Taylor, Scott Wood, Christina Xu, Kátia Nones, J. Lynn Fink, Angelika N. Christ, Tim Bruxner, Nicole Cloonan, Felicity Newell, John V. Pearson, Peter J. Bailey, Michael C. Quinn, Shivashankar H. Nagaraj, Stephen H. Kazakoff, Nick M. Waddell, Keerthana Krisnan, Kelly Quek, David Wood, Jaswinder S. Samra, Anthony J. Gill, Nick Pavlakis, Alex Guminski, Christopher W. Toon, Ray Asghari, Neil D. Merrett, Darren Pavey, Amitabha Das, Peter H. Cosman, Kasim Ismail, Chelsie O’Connnor, Vincent Lam, Duncan McLeod, Henry Pleass, A. J. Richardson, Virginia James, James G. Kench, Caroline Cooper, David Joseph, Charbel Sandroussi, Michael Crawford, James Gallagher, Michael Texler, Cindy Forest, Andrew Laycock, Krishna Epari, Mo Ballal, David Fletcher, Sanjay Mukhedkar, Nigel Spry, Bastiaan DeBoer, Ming Gene Chai, Nikolajs Zeps, Maria Beilin, Kynan Feeney, Nan Q. Nguyen, Andrew Ruszkiewicz, Chris Worthley, Chuan Ping Tan, Tamara Debrencini, John Chen, Mark E. Brooke-Smith, Virginia Papangelis, H.H.K. Tang, Andrew P. Barbour, Andrew D. Clouston, Patrick Martin, Thomas O’Rourke, Amy Chiang, J. Fawcett, Kellee Slater, Shinn Yeung, Michael Hatzifotis, Peter Hodgkinson, Christopher Christophi, Mehrdad Nikfarjam, A. Mountain, Victorian Cancer Biobank, James R. Eshleman, Ralph H. Hruban, Anirban Maitra, Christine A. Iacobuzio‐Donahue, Richard D. Schulick, Christopher L. Wolfgang, Richard A. Morgan, Mary Hodgin, Aldo Scarpa, Rita T. Lawlor, Stefania Beghelli, Vincenzo Corbo, Maria Scardoni, Claudio Bassi, Margaret A. Tempero, Andrew V. Biankin, Sean M. Grimmond, David K. Chang, Elizabeth A. Musgrove, Marc D. Jones, Craig Nourse, Nigel B. Jamieson, Janet Graham, Andrew V. Biankin, David K. Chang, Nigel B. Jamieson, Janet Graham
Software Mentions: 5
Published: almost 4 years ago
10.1107/S2052252518010552
Homology-based loop modeling yields more complete crystallographic protein structuresCited by: 25
Author(s): Bart van Beusekom, Krista Joosten, Maarten L. Hekkelman, Robbie P. Joosten, Anastassis Perrakis
Software Mentions: 2
Published: about 6 years ago