bioconductor: GEOmetadb | Projects

10.1093/bib/bbv080

Public data and open source tools for multi-assay genomic investigation of disease
Cited by: 47
Author(s): Lavanya Kannan, Marcel Ramos, Angela Re, Nehmé El-Hachem, Zhaleh Safikhani, Deena M.A. Gendoo, Sean Davis, David Gomez-Cabrero, Robert Castelo, Kasper D. Hansen, Vincent J. Carey, Martin Morgan, Aedín C. Culhane, Benjamin Haibe‐Kains, Levi Waldron
Software Mentions: 15
Published: almost 9 years ago

10.1186/s12864-021-07381-z

Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing
Cited by: 11
Author(s): Benjamin P. Kellman, Hratch Baghdassarian, Tiziano Pramparo, Isaac Shamie, Vahid H. Gazestani, Arjana Begzati, Shangzhong Li, Srinivasa Nalabolu, Sarah Murray, Linda Lopez, Karen Pierce, Eric Courchesne, Nathan E. Lewis
Software Mentions: 11
Published: over 3 years ago

10.1186/1756-0500-5-282

Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results
Cited by: 9
Author(s): Yilin Dai, Ling Guo, Meng Li, Yibu Chen
Software Mentions: 11
Published: over 12 years ago

10.3390/ijms19061808

Co-Expression Network Analysis of AMPK and Autophagy Gene Products during Adipocyte Differentiation
Cited by: 8
Author(s): Mahmoud Ahmed, Jin Seok Hwang, Trang Huyen Lai, Sahib Zada, Huynh Quoc Nguyen, Trang Min Pham, Miyong Yun, Deok Ryong Kim
Software Mentions: 7
Published: about 6 years ago

10.1186/s12859-018-2338-4

Data-driven human transcriptomic modules determined by independent component analysis
Cited by: 23
Author(s): Weizhuang Zhou, Russ B. Altman
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12859-019-2643-6

First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_
Cited by: 8
Author(s): Marco Moretto, Paolo Sonego, Ana B. Villasenõr-Altamirano, Kristof Engelen
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-020-57716-1

Ontology-driven integrative analysis of omics data through Onassis
Cited by: 9
Author(s): Eugenia Galeota, Kamal Kishore, Mattia Pelizzola
Software Mentions: 6
Published: over 4 years ago

10.18632/oncotarget.6679

Computational selection of antibody-drug conjugate targets for breast cancer
Cited by: 13
Author(s): François Fauteux, Jonathan D. Hill, María Jaramillo, Youlian Pan, Sieu Phan, Fazel Famili, Maureen D. O'Connor‐McCourt
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-019-6390-x

High-level integration of murine intestinal transcriptomics data highlights the importance of the complement system in mucosal homeostasis
Cited by: 8
Author(s): Nirupama Benis, Jerry M. Wells, M.A. Smits, Soumya K. Kar, Bart van der Hee, Vítor A. P. Martins dos Santos, María Suárez-Diez, Dirkjan Schokker
Software Mentions: 4
Published: almost 5 years ago

10.1093/bioinformatics/btu027

IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics
Cited by: 15
Author(s): Marta Rosikiewicz, Marc Robinson‐Rechavi
Software Mentions: 4
Published: over 10 years ago

10.1186/1471-2164-11-574

Heading Down the Wrong Pathway: on the Influence of Correlation within Gene Sets
Cited by: 74
Author(s): Daniel M. Gatti, William T. Barry, Andrew B. Nobel, Ivan Rusyn, Fred A. Wright
Software Mentions: 3
Published: almost 14 years ago

10.1186/1471-2105-11-421

Microarray meta-analysis database (M2DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database
Cited by: 35
Author(s): Wei‐Chung Cheng, Min-Lung Tsai, Cheng-Wei Chang, Ching-Lung Huang, Chaang-Ray Chen, Wun‐Yi Shu, Yun‐Shien Lee, Tzu‐Hao Wang, Ji-Hong Hong, Chia-Yang Li, Ian C. Hsu
Software Mentions: 3
Published: about 14 years ago

10.7717/peerj.5743

Effects of rheumatoid arthritis associated transcriptional changes on osteoclast differentiation network in the synovium
Cited by: 6
Author(s): Shilpa Harshan, Poulami Dey, Srivatsan Ragunathan
Software Mentions: 3
Published: almost 6 years ago

10.3390/microarrays5030023

Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories
Cited by: 9
Author(s): Sriram P. Chockalingam, Maneesha Aluru, Srinivas Aluru
Software Mentions: 3
Published: almost 8 years ago

10.3389/fbioe.2015.00038

Metabolonote: A Wiki-Based Database for Managing Hierarchical Metadata of Metabolome Analyses
Cited by: 33
Author(s): Takeshi Ara, Mitsuo Enomoto, Masanori Arita, Chiaki Ikeda, Kota Kera, Manabu Yamada, Takaaki Nishioka, Tasuku Ikeda, Yoshito Nihei, Daisuke Shibata, Shigehiko Kanaya, Nozomu Sakurai
Software Mentions: 3
Published: over 9 years ago

10.21203/rs.3.rs-100914/v1

Sex differences in viral entry protein expression, host responses to SARS-CoV-2, and in vitro responses to sex steroid hormone treatment in COVID-19
Cited by: 5
Author(s): Mengying Sun, Rama Shankar, Meehyun Ko, Christopher Daniel Chang, Shan-Ju Yeh, Shilong Li, Ke Liu, Guoli Zhou, Jing Xing, Austin VanVelsen, Tyler VanVelsen, Shreya Paithankar, Benjamin Y. Feng, Krista Young, Michael Strug, Lauren Turco, Zichen Wang, Eric E. Schadt, Rong Chen, Xiaohong Li, Tomiko Oskotsky, Marina Sirota, Benjamin S. Glicksberg, Girish N. Nadkarni, Adam J. Moeser, Li Li, Seungtaek Kim, Jiayu Zhou, Bin Chen
Software Mentions: 3
Published: almost 4 years ago

10.1093/database/bav099

<i>NeuroTransDB</i>: highly curated and structured transcriptomic metadata for neurodegenerative diseases
Cited by: 7
Author(s): Shweta Bagewadi, Subash Adhikari, Anjani Dhrangadhariya, Afroza Khanam Irin, Christian Ebeling, A Namasivayam, Matthew J. Page, Martin Hofmann‐Apitius, Philipp Senger
Software Mentions: 2
Published: over 9 years ago

10.1093/database/bay063

PtRFdb: a database for plant transfer RNA-derived fragments
Cited by: 28
Author(s): Nikita Gupta, Ajeet Singh, Shafaque Zahra, Shailesh Kumar
Software Mentions: 2
Published: over 6 years ago

10.1038/s41388-018-0588-2

LCE: an open web portal to explore gene expression and clinical associations in lung cancer
Cited by: 70
Author(s): Ling Cai, Shing-Jong Lin, Luc Girard, Yunyun Zhou, Lin Yang, Bo Ci, Qinbo Zhou, Danni Luo, Bo Yao, Jing Tang, Jeffrey D. Allen, Kenneth E. Huffman, Adi F. Gazdar, John V. Heymach, Ignacio I. Wistuba, Guanghua Xiao, John D. Minna, Yang Xie
Software Mentions: 2
Published: almost 6 years ago

10.1093/database/bay135

AtFusionDB: a database of fusion transcripts in<i>Arabidopsis thaliana</i>
Cited by: 6
Author(s): Ajeet Singh, Shafaque Zahra, Durdam Das, Shailesh Kumar
Software Mentions: 2
Published: over 5 years ago

10.1093/database/bay145

Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis
Cited by: 18
Author(s): Guocai Chen, Juan Camilo Ramírez, Nan Deng, Xing Qiu, Canglin Wu, W. Jim Zheng, Hulin Wu
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pbio.2002477

Wide-Open: Accelerating public data release by automating detection of overdue datasets
Cited by: 10
Author(s): Maxim Grechkin, Hoifung Poon, Bill Howe
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-10-S3-S15

Improving gene expression similarity measurement using pathway-based analytic dimension
Cited by: 4
Author(s): Changwon Keum, Jung Hoon Woo, Won Seok Oh, Sue-Nie Park, Kyoung Tai No
Software Mentions: 2
Published: almost 15 years ago

10.1186/s12859-017-1888-1

ALE: automated label extraction from GEO metadata
Cited by: 19
Author(s): Cory B. Giles, Chase A. Brown, Michael Ripperger, Zane Dennis, Xiavan Roopnarinesingh, Hunter Porter, Aleksandra Perz, Jonathan D. Wren
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pcbi.1002090

An Evolutionary Trade-Off between Protein Turnover Rate and Protein Aggregation Favors a Higher Aggregation Propensity in Fast Degrading Proteins
Cited by: 52
Author(s): Greet De Baets, Joke Reumers, Javier Delgado, Joaquı́n Dopazo, Joost Schymkowitz, Frédéric Rousseau
Software Mentions: 1
Published: about 13 years ago

10.12688/f1000research.8182.2

A curated compendium of monocyte transcriptome datasets of relevance to human monocyte immunobiology research
Cited by: 18
Author(s): Darawan Rinchai, Sabri Boughorbel, Scott Presnell, Charlie Quinn, Damien Chaussabel
Software Mentions: 1
Published: over 8 years ago

10.1155/2015/318064

MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies
Cited by: 4
Author(s): Pankaj Kumar, Anna Halama, Shahina Hayat, Anja M. Billing, Manish Gupta, Noha A. Yousri, Gregory Smith, Karsten Suhre
Software Mentions: 1
Published: over 9 years ago

Ecosyste.ms: Papers

Projects: bioconductor: GEOmetadb

Papers Mentioning GEOmetadb 27