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.

Papers: 10.1016/j.cell.2019.10.007

https://doi.org/10.1016/j.cell.2019.10.007

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

Cited by: 375
Author(s): David Clark, Saravana M. Dhanasekaran, Francesca Petralia, Jianbo Pan, Xiaoyu Song, Yingwei Hu, Felipe da Veiga Leprevost, Boris Reva, Tung-Shing Mamie Lih, Hui-Yin Chang, Wanli Ma, Chen Huang, Christopher J. Ricketts, Lijun Chen, Azra Krek, Yize Li, Dmitry Rykunov, Qing Kay Li, Lin S. Chen, Umut Özbek, Suhas Vasaikar, Yige Wu, Seungyeul Yoo, Shrabanti Chowdhury, Matthew A. Wyczalkowski, Jiayi Ji, Michael Schnaubelt, Andy T. Kong, Sunantha Sethuraman, Dmitry M. Avtonomov, Minghui Ao, Antonio Colaprico, Song Cao, Kyung-Cho Cho, Selim Kalayci, Shiyong Ma, Wenke Liu, Kelly V. Ruggles, Anna Calinawan, Zeynep H. Gümüş, Daniel Geiszler, Emily Kawaler, Guo Ci Teo, Bo Wen, Yuping Zhang, Sarah Keegan, Kai Li, Feng Chen, Nathan Edwards, Phillip M. Pierorazio, Xi Steven Chen, Christian P. Pavlovich, A. Ari Hakimi, Gabriel Bromiński, James J. Hsieh, Andrzej Antczak, Tatiana Omelchenko, Jan Lubiński, Maciej Wiznerowicz, W. Marston Linehan, Christopher R. Kinsinger, Mathangi Thiagarajan, Emily S. Boja, Mehdi Mesri, Tara Hiltke, Ana I. Robles, Henry Rodriguez, Jiang Qian, David Fenyö, Bing Zhang, Ding Li, Eric E. Schadt, Arul M. Chinnaiyan, Zhen Zhang, Gilbert S. Omenn, Marcin Cieślik, Daniel W. Chan, Alexey I. Nesvizhskii, Pei Wang, Hui Zhang, A. Samad Hashimi, Alexander Pico, Alla Karpova, Alyssa Charamut, Amanda G. Paulovich, Amy M. Perou, Anna Malovannaya, Annette Marrero-Oliveras, Anupriya Agarwal, Barbara Hindenach, Barbara L. Pruetz, Beom-Jun Kim, Brian J. Druker, Chelsea J. Newton, Chet Birger, Corbin D. Jones, Cristina E. Tognon, D. R. Mani, Dana R. Valley, Daniel C. Rohrer, Daniel Cui Zhou, Darlene Tansil, David Chesla, David I. Heiman, David A. Wheeler, Donghui Tan, Doug W. Chan, Emek Demir, Ewa Malc, Francesmary Modugno, Gaddy Getz, Galen Hostetter, George Wilson, Gerald W. Hart, Heng Zhu, Hongwei Liu, Houston Culpepper, Hua Sun, Hua Zhou, Jacob Day, James Suh, Jasmine Huang, Jason McDermott, Jeffrey R. Whiteaker, Jeffrey W. Tyner, Jennifer Eschbacher, Jin Chen, John P. McGee, Jun Zhu, Karen A. Ketchum, Karin D. Rodland, Karl R. Clauser, Karna Robinson, Karsten Krug, Katherine A. Hoadley, Ki Sung Um, Kim Elburn, Kimberly Holloway, Liang-Bo Wang, Lili M. Blumenberg, Linda Hannick, Liqun Qi, Lori J. Sokoll, MacIntosh Cornwell, Marc Loriaux, Marcin J. Domagalski, Marina Gritsenko, Matthew L. Anderson, Matthew E. Monroe, Matthew J. Ellis, Maureen A. Dyer, Meenakshi Anurag, Meghan C. Burke, Melissa Borucki, Michael A. Gillette, Michael J. Birrer, Michael R. Lewis, Michael Ittmann, Michael J. Smith, Michael Vernon, Michelle Chaikin, Milan G. Chheda, Munziba Khan, Nancy Roche, Nathan Edwards, Negin Vatanian, Nicole Tignor, Noam D. Beckmann, Pamela Grady, Patricia Castro, Paul Piehowski, Peter B. McGarvey, Piotr A. Mieczkowski, Pushpa Hariharan, Qingsong Gao, Rajiv Dhir, Ramani B. Kothadia, Ratna R. Thangudu, Rebecca Montgomery, Reyka G. Jayasinghe, Richard Smith, Robert A. Edwards, Robert Zelt, Ross M. Bremner, Ruiyang Liu, Runyu Hong, Sailaja Mareedu, Samuel H. Payne, Sandra Cottingham, Sanford P. Markey, Scott D. Jewell, Shalin Patel, Shankha Satpathy, Shannon Richey, Sherri R. Davies, Shuang Cai, Simina M. Boca, Snehal Patil, Sohini Sengupta, Sonya Carter, Stacey Gabriel, Stefani N. Thomas, Stephanie Young, Stephen E. Stein, Steven A. Carr, Steven M. Foltz, S. G. Hilsenbeck, Tanya Krubit, Tao Liu, Tara Skelly, Thomas F. Westbrook, Uma Borate, Uma Velvulou, Vladislav Petyuk, William Bocik, Xi Chen, Yan Shi, Yifat Geffen, Yihao Lu, Ying Wang, Yosef E. Maruvka, Zhi Li, Zhiao Shi, Zhidong Tu
Published: about 5 years ago

Software Mentions 10

bioconductor: CancerSubtypes
Cancer subtypes identification, validation and visualization based on multiple genomic data sets
Papers that mentioned: 22
bioconductor: ConsensusClusterPlus
ConsensusClusterPlus
Papers that mentioned: 313
bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in R
Papers that mentioned: 6,568
bioconductor: GSVA
Gene Set Variation Analysis for microarray and RNA-seq data
Papers that mentioned: 893
bioconductor: PureCN
Copy number calling and SNV classification using targeted short read sequencing
Papers that mentioned: 11
bioconductor: TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
Papers that mentioned: 276
cran: gelnet
Generalized Elastic Nets
Papers that mentioned: 3
cran: STAR
Spike Train Analysis with R
Papers that mentioned: 5,759
cran: WebGestaltR
Gene Set Analysis Toolkit WebGestaltR
Papers that mentioned: 30
pypi: GSVA
Python CLI and module for running the GSVA R bioconductor package with Python Pandas inputs and outputs.
Papers that mentioned: 893