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: RTCGAToolbox

https://packages.ecosyste.ms/registries/bioconductor.org/packages/RTCGAToolbox

A new tool for exporting TCGA Firehose data
1 version
Latest release: 10 months ago
2 dependent packages
61,941 downloads total

Papers Mentioning RTCGAToolbox 22

10.12688/f1000research.8923.2

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
Cited by: 105
Author(s): Tiago C. Silva, Antonio Colaprico, Catharina Olsen, Fulvio D’Angelo, Gianluca Bontempi, Michele Ceccarelli, Houtan Noushmehr
Software Mentions: 17
Published: over 7 years ago

10.3389/fgene.2020.522125

Identification of Prognostic Markers in Cholangiocarcinoma Using Altered DNA Methylation and Gene Expression Profiles
Cited by: 11
Author(s): Nitish K. Mishra, Meng Niu, Siddesh Southekal, Prachi Bajpai, Amr Elkholy, Upender Manne, Chittibabu Guda
Software Mentions: 14
Published: almost 4 years ago

10.1186/s12920-017-0261-6

CVE: an R package for interactive variant prioritisation in precision oncology
Cited by: 6
Author(s): Andreas Möck, Suzanne Murphy, James A. Morris, Francesco Marass, Nitzan Rosenfeld, Charles E. Massie
Software Mentions: 14
Published: about 7 years ago

10.3390/biomedicines8110488

TCox: Correlation-Based Regularization Applied to Colorectal Cancer Survival Data
Cited by: 4
Author(s): Carolina Peixoto, Marta B. Lopes, Marta Martins, Luís Costa, Susana Vinga
Software Mentions: 11
Published: over 3 years ago

10.1093/database/baw160

FirebrowseR: an R client to the Broad Institute’s Firehose Pipeline
Cited by: 123
Author(s): Mario C. Deng, Johannes Brägelmann, Ivan Kryukov, Nuno Saraiva-Agostinho, Sven Perner
Software Mentions: 7
Published: over 7 years ago

10.18632/oncotarget.15993

Genome-wide DNA methylation analysis reveals molecular subtypes of pancreatic cancer
Cited by: 67
Author(s): Nitish K. Mishra, Chittibabu Guda
Software Mentions: 7
Published: over 7 years ago

10.1371/journal.pone.0106397

RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data
Cited by: 138
Author(s): Mehmet K. Samur
Software Mentions: 6
Published: almost 10 years ago

10.1155/2020/3451610

A Pipeline to Call Multilevel Expression Changes between Cancer and Normal Tissues and Its Applications in Repurposing Drugs Effective for Gastric Cancer
Cited by: 3
Author(s): Wei Gao, Jun Yang, Changhua Zhuo, Sha Huang, Lin Jia, Guangfeng Wu, Min Zhou
Software Mentions: 5
Published: almost 4 years ago

10.1002/1878-0261.12838

SIK2 represses AKT/GSK3β/β‐catenin signaling and suppresses gastric cancer by inhibiting autophagic degradation of protein phosphatases
Cited by: 17
Author(s): Xiaoman Dai, Yan‐hui Zhang, Xiaohong Lin, Xiaoxing Huang, Yi Zhang, Chaorong Xue, Wan-Nan Chen, Jian‐xin Ye, Xi Zhang Lin, Xu Lin
Software Mentions: 5
Published: over 3 years ago

10.1186/s12885-016-2948-z

Conservation of immune gene signatures in solid tumors and prognostic implications
Cited by: 62
Author(s): Julia Chifman, Ashok Pullikuth, Jeff W. Chou, Davide Bedognetti, Lance D. Miller
Software Mentions: 4
Published: over 7 years ago

10.15252/emmm.201708428

Comparative proteomics reveals a diagnostic signature for pulmonary head‐and‐neck cancer metastasis
Cited by: 41
Author(s): Hanibal Bohnenberger, Lars Kaderali, Philipp Ströbel, Diego Yepes, Uwe Plessmann, Neekesh V. Dharia, Sha Yao, Carina Heydt, Sabine Merkelbach‐Bruse, Alexander Emmert, Jonatan F. Hoffmann, Julius Bodemeyer, Kirsten Reuter‐Jessen, Anna‐Maria Lois, Leif Hendrik Dröge, Philipp Baumeister, Christoph Walz, Lorenz Biggemann, Roland B. Walter, Björn Häupl, Federico Comoglio, Kuan‐Ting Pan, Sebastian Scheich, Christof Lenz, Stefan Küffer, Felix Bremmer, Julia Kitz, Maren Sitte, Tim Beißbarth, Marc Hinterthaner, Martin Sebastian, Joachim Lotz, Hans‐Ulrich Schildhaus, Hendrik A. Wolff, Bernhard C. Danner, Christian Brandts, Reinhard Büttner, Martin Canis, Kimberly Stegmaier, Hubert Serve, Henning Urlaub, Thomas Oellerich
Software Mentions: 4
Published: almost 6 years ago

10.1093/gigascience/giz045

A multi-omics data simulator for complex disease studies and its application to evaluate multi-omics data analysis methods for disease classification
Cited by: 24
Author(s): Ren‐Hua Chung, Chen-Yu Kang
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-41015-5

Burden of unique and low prevalence somatic mutations correlates with cancer survival
Cited by: 45
Author(s): Nikolai Klebanov, Mykyta Artomov, William B. Goggins, Eoin Daly, Mark J. Daly, Hensin Tsao
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-39891-y

The impact of estimated tumour purity on gene expression-based drug repositioning of Clear Cell Renal Cell Carcinoma samples
Cited by: 6
Author(s): Karel K.M. Koudijs, Anton G.T. Terwisscha van Scheltinga, Stefan Böhringer, Kirsten J. M. Schimmel, Henk‐Jan Guchelaar
Software Mentions: 3
Published: over 5 years ago

10.7150/jca.32768

Aldo-Keto Reductase Family 1 Member B10 (AKR1B10) overexpression in tumors predicts worse overall survival in hepatocellular carcinoma
Cited by: 15
Author(s): Jia Shi, Lixiang Chen, Yi Chen, Yao Lu, Xiaorong Chen, Zongguo Yang
Software Mentions: 2
Published: over 5 years ago

10.1038/s41416-018-0109-7

Cancer subtype identification using somatic mutation data
Cited by: 46
Author(s): Marieke L. Kuijjer, Joseph N. Paulson, Peter Salzman, Wei Ding, John Quackenbush
Software Mentions: 2
Published: about 6 years ago

10.7150/jca.40237

Prognostic gene expression signature revealed the involvement of mutational pathways in cancer genome
Cited by: 15
Author(s): Hongde Liu, Huamei Li, Kun Luo, Ingo G. H. Schmidt‐Wolf, Xiao Xin Sun
Software Mentions: 1
Published: over 4 years ago

10.3390/cancers11101600

Mutational Landscape of the BAP1 Locus Reveals an Intrinsic Control to Regulate the miRNA Network and the Binding of Protein Complexes in Uveal Melanoma
Cited by: 29
Author(s): Ingo G. H. Schmidt‐Wolf, Arijit Biswas, Hongde Liu, Sagnik Sen, Anoosha Paruchuri, Panagiotis Katsonis, Olivier Lichtarge, Tikam Chand Dakal, Ujjwal Maulik, M. Michael Gromiha, Sanghamitra Bandyopadhyay, Michael Ludwig, Frank G. Holz, Karin U. Loeffler, Martina C. Herwig‐Carl
Software Mentions: 1
Published: almost 5 years ago

10.1155/2020/9696285

Construction and Investigation of an LINC00284-Associated Regulatory Network in Serous Ovarian Carcinoma
Cited by: 8
Author(s): Shasha Wang, Lu Zhang, Tao Lin, Lijuan Pang, Ruiting Fu, Yu Fu, Wei Liang, Yaobin Ding, Wei Hua Jia
Software Mentions: 1
Published: over 4 years ago

10.1155/2019/2867372

Overexpression of ICAM-1 Predicts Poor Survival in High-Grade Serous Ovarian Carcinoma: A Study Based on TCGA and GEO Databases and Tissue Microarray
Cited by: 6
Author(s): Shasha Wang, Can Yin, Ying Zhang, Lu Zhang, Tao Lin, Wei Liang, Lijuan Pang, Ruiting Fu, Yaobin Ding, Feng Li, Wei Hua Jia
Software Mentions: 1
Published: about 5 years ago

10.1042/BSR20211370

Prostasin regulates PD-L1 expression in human lung cancer cells
Cited by: 1
Author(s): Limei Chen, Julius C Chai, Bin Liu, Tara M. Strutt, K. Kai McKinstry, Karl X. Chai
Software Mentions: 1
Published: about 3 years ago

10.3892/ol.2020.12077

Identification of hub genes associated with esophageal cancer progression using bioinformatics analysis
Cited by: 3
Author(s): Jiangfen Li, Yufang Xie, Xueli Wang, Cuncang Jiang, Xin Yuan, Anzhi Zhang, Lan Yang, Chunxia Liu, Hong Zou, Feng Li, Jianming Hu
Software Mentions: 1
Published: almost 4 years ago