bioconductor: GSCA | Projects | Ecosyste.ms: Papers

10.3389/fgene.2019.00594

BioNetStat: A Tool for Biological Networks Differential Analysis
Cited by: 21
Author(s): Vinícius Carvalho Jardim, Suzana de Siqueira Santos, André Fujita, Marcos Silveira Buckeridge
Software Mentions: 22
Published: over 5 years ago

10.1371/journal.pone.0135831

CoGA: An R Package to Identify Differentially Co-Expressed Gene Sets by Analyzing the Graph Spectra
Cited by: 18
Author(s): Suzana de Siqueira Santos, Thais Fernanda de Almeida Galatro, Rodrigo Akira Watanabe, Sueli Mieko Oba-Shinjo, Suely Kazue Nagahashi Marie, André Fujita
Software Mentions: 17
Published: about 9 years ago

10.3389/fcell.2021.709022

Identification of the Role and Clinical Prognostic Value of Target Genes of m6A RNA Methylation Regulators in Glioma
Cited by: 24
Author(s): Peilin Cong, Tingmei Wu, Xinwei Huang, Huazheng Liang, Xiaofei Gao, Li Tian, Wanrong Li, Aiwen Chen, Hanxi Wan, Mengfan He, Danqing Dai, Zhen Li, Lize Xiong
Software Mentions: 13
Published: about 3 years ago

10.1186/s12935-021-01795-1

Identification and development of a novel invasion-related gene signature for prognosis prediction in colon adenocarcinoma
Cited by: 15
Author(s): Jiahua Liu, Chunhui Jiang, Chunjie Xu, Dongyang Wang, Ya Shen, Ye Liu, Lei Gu
Software Mentions: 11
Published: almost 4 years ago

10.1155/2021/7404927

A Comprehensive Multiomics Analysis Identified Ubiquilin 4 as a Promising Prognostic Biomarker of Immune-Related Therapy in Pan-Cancer
Cited by: 4
Author(s): Jie Li, Ye Tong, Zhi Wang, Yi Liu, Xiaofeng Dai, Yubing Zhu
Software Mentions: 10
Published: about 3 years ago

10.1186/s12918-016-0349-1

DGCA: A comprehensive R package for Differential Gene Correlation Analysis
Cited by: 156
Author(s): Andrew McKenzie, Igor Katsyv, Won Min Song, Minghui Wang, Bin Zhang
Software Mentions: 9
Published: about 8 years ago

10.3389/fonc.2021.674394

Comprehensive Analysis of Cyclin Family Gene Expression in Colon Cancer
Cited by: 12
Author(s): Jieling Li, Liyuan Zhou, Ying Liu, Lingzhi Yang, Dayi Jiang, Kuan Li, Shouqi Xie, Wang Xiao, Shaoxiang Wang
Software Mentions: 7
Published: over 3 years ago

10.3389/fonc.2021.632459

Construction and Validation of a Novel Eight-Gene Risk Signature to Predict the Progression and Prognosis of Bladder Cancer
Cited by: 3
Author(s): Ruiliang Wang, Zongtai Zheng, Shun Mao, Wentao Zhang, Ji Liu, Cheng Li, Shenghua Liu, Xudong Yao
Software Mentions: 7
Published: over 3 years ago

10.1186/s12864-019-6155-6

A framework using topological pathways for deeper analysis of transcriptome data
Cited by: 0
Author(s): Yue Zhao, Stephanie Piekos, Tham H. Hoang, Dong-Guk Shin
Software Mentions: 7
Published: over 4 years ago

10.3390/genes12050665

Rewired Pathways and Disrupted Pathway Crosstalk in Schizophrenia Transcriptomes by Multiple Differential Coexpression Methods
Cited by: 6
Author(s): Hui Yu, Yan Guo, Jingchun Chen, Xiangning Chen, Peilin Jia, Zhongming Zhao
Software Mentions: 6
Published: over 3 years ago

10.1186/s12859-017-1482-6

GSAR: Bioconductor package for Gene Set analysis in R
Cited by: 34
Author(s): Yasir Rahmatallah, Boris Zybailov, Frank Emmert‐Streib, Galina Glazko
Software Mentions: 6
Published: almost 8 years ago

10.3389/fgene.2021.647653

DysPIA: A Novel Dysregulated Pathway Identification Analysis Method
Cited by: 1
Author(s): Limei Wang, Weixin Xie, Kongning Li, Zhenzhen Wang, Xia Li, Weixing Feng, Li Jin
Software Mentions: 6
Published: over 3 years ago

10.3389/fgene.2020.00654

Gene Set Analysis: Challenges, Opportunities, and Future Research
Cited by: 98
Author(s): Farhad Maleki, Katie Ovens, Daniel J. Hogan, Anthony Kusalik
Software Mentions: 5
Published: over 4 years ago

10.1186/s12859-016-0928-6

Gene set analysis using sufficient dimension reduction
Cited by: 7
Author(s): Huey-Miin Hsueh, Tsai Chen-An
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pcbi.1008976

MetaGSCA: A tool for meta-analysis of gene set differential coexpression
Cited by: 2
Author(s): Yan Guo, Hui Yu, Haocan Song, Jia-Peng He, Olufunmilola Oyebamiji, Huining Kang, Jie Ping, Scott A. Ness, Yu Shyr, Fei Ye
Software Mentions: 5
Published: over 3 years ago

10.1186/s13073-017-0492-3

Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists
Cited by: 63
Author(s): Xun Zhu, Thomas Wolfgruber, Austin Tasato, Cédric Arisdakessian, David Garmire, Lana X. Garmire
Software Mentions: 5
Published: almost 7 years ago

10.1111/jcmm.16818

The role of YTH domain containing 2 in epigenetic modification and immune infiltration of pan‐cancer
Cited by: 16
Author(s): Chiyuan Zhang, Cuishan Guo, Yan Li, Liang Ouyang, Qi Zhao, Kuiran Liu
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2021.630215

Comparing Statistical Tests for Differential Network Analysis of Gene Modules
Cited by: 2
Author(s): Jaron Arbet, Yaxu Zhuang, Elizabeth Litkowski, Laura Saba, Katerina Kechris
Software Mentions: 4
Published: over 3 years ago

10.1186/s13104-020-05357-y

Comprehensive analysis of single-cell RNA sequencing data from healthy human marrow hematopoietic cells
Cited by: 4
Author(s): Xin Zhao, Shaojian Gao, Sachiko Kajigaya, Qingguo Liu, Zhijie Wu, Xingmin Feng, Fengkui Zhang, Neal S. Young
Software Mentions: 4
Published: about 4 years ago

10.1186/s12920-020-00772-3

Expression correlation attenuates within and between key signaling pathways in chronic kidney disease
Cited by: 9
Author(s): Hui Yu, Dan-Qian Chen, Olufunmilola Oyebamiji, Zhao Yan, Yan Guo
Software Mentions: 4
Published: about 4 years ago

10.3389/fpsyg.2017.00916

Model Evaluation in Generalized Structured Component Analysis Using Confirmatory Tetrad Analysis
Cited by: 6
Author(s): Ji Hoon Ryoo, Heungsun Hwang
Software Mentions: 3
Published: over 7 years ago

10.1186/s13045-020-00854-w

Identification of cross-talk between m6A and 5mC regulators associated with onco-immunogenic features and prognosis across 33 cancer types
Cited by: 44
Author(s): Yutong Chen, Jiayi Shen, Dongping Chen, Chengdong Wu, Rui Guo, Panpan Zhang, Jiawei Lv, Wenfei Li, Zi‐Xian Wang, Yu-Pei Chen
Software Mentions: 3
Published: over 4 years ago

10.1042/BSR20210055

Early B-cell factors involve in the tumorigenesis and predict the overall survival of gastric cancer
Cited by: 3
Author(s): Qing Wang, Jiahong Liang, Xianyu Hu, Shen Gu, Qingdong Xu, Yan Jiang
Software Mentions: 3
Published: over 3 years ago

10.3389/fpsyg.2018.02461

A Comparative Study on the Performance of GSCA and CSA in Parameter Recovery for Structural Equation Models With Ordinal Observed Variables
Cited by: 8
Author(s): Kwanghee Jung, Pavel Panko, Jae‐Hoon Lee, Heungsun Hwang
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12859-018-2066-9

Pathway-based approach using hierarchical components of rare variants to analyze multiple phenotypes
Cited by: 5
Author(s): Sung Young Lee, Yongkang Kim, Sungkyoung Choi, Heungsun Hwang, Taesung Park
Software Mentions: 3
Published: over 6 years ago

10.12688/wellcomeopenres.14677.4

Stage 2 Registered Report: Variation in neurodevelopmental outcomes in children with sex chromosome trisomies: testing the double hit hypothesis
Cited by: 0
Author(s): Dianne F. Newbury, Nuala H. Simpson, Paul A. Thompson, Dorothy V. M. Bishop
Software Mentions: 2
Published: over 3 years ago

10.3390/cells10081970

Comprehensive Omics Analysis of a Novel Small-Molecule Inhibitor of Chemoresistant Oncogenic Signatures in Colorectal Cancer Cell with Antitumor Effects
Cited by: 6
Author(s): Ting‐Hsiang Huang, Ntlotlang Mokgautsi, Yan‐Jiun Huang, Alexander T.H. Wu, Hsu‐Shan Huang
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2021.690990

Identification and Validation of Potential Candidate Genes of Colorectal Cancer in Response to Fusobacterium nucleatum Infection
Cited by: 0
Author(s): Jiangguo Zhang, Zhimo Wang, Hong Liu, Guojun Li
Software Mentions: 2
Published: about 3 years ago

10.12688/wellcomeopenres.15396.2

Generalized Structured Component Analysis in candidate gene association studies: applications and limitations
Cited by: 1
Author(s): Paul A. Thompson, Dorothy V. M. Bishop, Else Eising, Simon E. Fisher, Dianne F. Newbury
Software Mentions: 2
Published: about 4 years ago

10.3390/ijms21186724

HisCoM-G×E: Hierarchical Structural Component Analysis of Gene-Based Gene–Environment Interactions
Cited by: 2
Author(s): Sungkyoung Choi, Sung Young Lee, Iksoo Huh, Heungsun Hwang, Taesung Park
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pcbi.1002955

Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression
Cited by: 146
Author(s): David Amar, Hershel M. Safer, Ron Shamir
Software Mentions: 1
Published: over 11 years ago

10.1016/j.exphem.2012.11.008

Gene set control analysis predicts hematopoietic control mechanisms from genome-wide transcription factor binding data
Cited by: 15
Author(s): Anagha Joshi, Rebecca Hannah, Evangelia Diamanti, Berthold Göttgens
Software Mentions: 1
Published: over 11 years ago

10.1016/j.omto.2021.06.014

TBC1D3 family is a prognostic biomarker and correlates with immune infiltration in kidney renal clear cell carcinoma
Cited by: 8
Author(s): Bei Wang, Dandan Chen, Haiying Hua
Software Mentions: 1
Published: about 3 years ago

10.1093/bioinformatics/btt687

Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets
Cited by: 90
Author(s): Yasir Rahmatallah, Frank Emmert‐Streib, Galina Glazko
Software Mentions: 1
Published: almost 11 years ago

10.3389/fpsyg.2019.02215

Comparison of Bootstrap Confidence Interval Methods for GSCA Using a Monte Carlo Simulation
Cited by: 57
Author(s): Kwanghee Jung, Jae‐Hoon Lee, Vibhuti Gupta, Gyeongcheol Cho
Software Mentions: 1
Published: about 5 years ago

10.3389/fpsyg.2017.02137

Generalized Structured Component Analysis with Uniqueness Terms for Accommodating Measurement Error
Cited by: 34
Author(s): Heungsun Hwang, Yoshio Takane, Kwanghee Jung
Software Mentions: 1
Published: almost 7 years ago

10.3389/fpsyg.2018.00332

Comparison of Methods for Factor Invariance Testing of a 1-Factor Model With Small Samples and Skewed Latent Traits
Cited by: 14
Author(s): Holmes Finch, Brian F. French, Maria E. Hernández Finch
Software Mentions: 1
Published: over 6 years ago

10.1093/schbul/sbu014

Symptom Dimensions of the Psychotic Symptom Rating Scales in Psychosis: A Multisite Study
Cited by: 87
Author(s): Todd S. Woodward, Kwanghee Jung, Heungsun Hwang, John Yin, Laura D. Taylor, Mahesh Menon, Emmanuelle Peters, Elizabeth Kuipers, Flavie Waters, Tania Lecomte, Iris Sommer, Kirstin Daalman, Remko van Lutterveld, D Hubl, Jochen Kindler, Philipp Homan, Johanna C. Badcock, Saruchi Chhabra, Matteo Cella, Sarah Keedy, Paul Allen, Andrea Mechelli, Antonio Preti, Sara Siddi, David H. Erickson
Software Mentions: 1
Published: over 10 years ago

10.1038/srep09634

Discerning mechanistically rewired biological pathways by cumulative interaction heterogeneity statistics
Cited by: 4
Author(s): Travis B. Cotton, Hien Nguyen, Joseph I. Said, Zhengyu Ouyang, Jinfa Zhang, Mingzhou Song
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0247592

A knowledge-based multivariate statistical method for examining gene-brain-behavioral/cognitive relationships: Imaging genetics generalized structured component analysis
Cited by: 4
Author(s): Heungsun Hwang, Gyeongcheol Cho, Min Jin, Ji Hoon Ryoo, Younyoung Choi, Seung Hwan Lee
Software Mentions: 1
Published: over 3 years ago

Projects: bioconductor: GSCA

Papers Mentioning GSCA 40