Projects: bioconductor: limma
https://packages.ecosyste.ms/registries/bioconductor.org/packages/limma
Linear Models for Microarray Data
3 versions
Latest release: over 1 year ago
314 dependent packages
4,663,292 downloads total
Science Score: 78/100
Starting Score: 100 points
Bonuses:
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+8
Academic maintainer emails
1 maintainers with academic email addresses
Penalties:
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-30
Corporate indicators
1 corporate/proprietary indicators found
Very Likely Science (78)
Papers Mentioning limma 7,776
10.1186/s13058-016-0758-5
Patient survival and tumor characteristics associated with CHEK2:p.I157T – findings from the Breast Cancer Association ConsortiumCited by: 37
Author(s): Taru Muranen, Carl Blomqvist, Thilo Dörk, Anna Jakubowska, Päivi Heikkilä, Rainer Fagerholm, Dario Greco, Kristiina Aittomäki, Stig E. Bojesen, Mitul Shah, Alison M. Dunning, Valerie Rhenius, Per Hall, Kamila Czene, Judith S. Brand, Hatef Darabi, Jenny Chang–Claude, Anja Rudolph, Børge G. Nordestgaard, Fergus J. Couch, Steven N. Hart, Jonine D. Figueroa, Montserrat García‐Closas, Peter A. Fasching, Matthias W. Beckmann, Jingmei Li, Jing Liu, Irene L. Andrulis, Robert Winqvist, Katri Pylkäs, Arto Mannermaa, Vesa Kataja, Annika Lindblom, Sara Margolin, Jan Lubiński, Natalia Dubrowinskaja, Manjeet K. Bolla, Joe Dennis, Kyriaki Michailidou, Qin Wang, Douglas F. Easton, Paul D.P. Pharoah, Marjanka K. Schmidt, Heli Nevanlinna
Software Mentions: 8
Published: almost 9 years ago
10.1038/s41598-018-24758-5
Applications of Bayesian network models in predicting types of hematological malignanciesCited by: 47
Author(s): Rupesh Agrahari, Amir Foroushani, T. Roderick Docking, Linda Chang, Gerben Duns, Monika Hudoba, Aly Karsan, Habil Zare
Software Mentions: 8
Published: about 7 years ago
10.1371/journal.pone.0143970
A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren’s SyndromeCited by: 37
Author(s): Katherine James, Shereen Al-Ali, Jessica Tarn, Simon Cockell, Colin S. Gillespie, Victoria Hindmarsh, James Locke, Sheryl Mitchell, Dennis Lendrem, Simon Bowman, Elizabeth Price, Colin Pease, Paul Emery, Peter Lanyon, John Hunter, Monica Gupta, Michèle Bombardieri, Nurhan Sutcliffe, Costantino Pitzalis, John McLaren, Annie Cooper, Marian Regan, Ian Giles, David Isenberg, Vadivelu Saravanan, David Coady, Bhaskar Dasgupta, Neil McHugh, Steven Young-Min, Robert J. Moots, Nagui Gendi, Mohammed Akil, Bridget Griffiths, Anil Wipat, Julia L. Newton, David Jones, John D. Isaacs, Jennifer Hallinan, Wan‐Fai Ng
Software Mentions: 8
Published: over 9 years ago
10.1371/journal.pgen.1009744
The Integrity of the HMR complex is necessary for centromeric binding and reproductive isolation in DrosophilaCited by: 25
Author(s): A. Lukacs, Andreas W. Thomae, P. Krueger, Tamás Schauer, Anuroop Venkateswaran Venkatasubramani, Natalia Y. Kochanova, Wasim Aftab, Rupam Choudhury, Ignasi Forné, Axel Imhof
Software Mentions: 8
Published: almost 4 years ago
10.7150/ijms.51064
Tumor Mutation Burden, Immune Cell Infiltration, and Construction of Immune-Related Genes Prognostic Model in Head and Neck CancerCited by: 32
Author(s): Aimin Jiang, Mengdi Ren, Na Liu, Huan Gao, Jingjing Wang, Xiaoqiang Zheng, Xiao Fu, Xuan Liu, Zhiping Ruan, Tao Tian, Yu Yao
Software Mentions: 8
Published: over 4 years ago
10.3389/fimmu.2020.00611
Human Regulatory T Cells From Umbilical Cord Blood Display Increased Repertoire Diversity and Lineage Stability Relative to Adult Peripheral BloodCited by: 19
Author(s): Keshav Motwani, Leeana D. Peters, Willem H Vliegen, Ahmed G Elsayed, Howard R. Seay, Maria-Cecilia Lopez, Henry V. Baker, Amanda L. Posgai, Todd M. Brusko, Daniel J. Perry, Rhonda Bacher, Joseph Larkin, Michael J. Haller
Software Mentions: 8
Published: over 5 years ago
10.1371/journal.pone.0159921
BEclear: Batch Effect Detection and Adjustment in DNA Methylation DataCited by: 19
Author(s): Ruslan Akulenko, Markus Merl, Volkhard Helms
Software Mentions: 8
Published: almost 9 years ago
10.1038/s41598-020-75541-4
Stromal microenvironment promoted infiltration in esophageal adenocarcinoma and squamous cell carcinoma: a multi-cohort gene-based analysisCited by: 6
Author(s): Jiali Li, Zhao-Yi Zeng, Xueping Jiang, Nannan Zhang, Yanping Gao, Yuan Luo, Wenjie Sun, Shuying Li, Jiangbo Ren, Yan Gong, Conghua Xie
Software Mentions: 8
Published: over 4 years ago
10.7150/ijms.48244
Identification of Key Genes and Pathways in Myeloma side population cells by Bioinformatics AnalysisCited by: 21
Author(s): Yang Qin, Kaihu Li, Xin Li, Jing Liu
Software Mentions: 8
Published: over 5 years ago
10.3233/JAD-170011
Analytical Strategy to Prioritize Alzheimer’s Disease Candidate Genes in Gene Regulatory Networks Using Public Expression DataCited by: 17
Author(s): Shweta Bagewadi Kawalia, Tamara Raschka, Mufassra Naz, Ricardo de Matos Simoes, Philipp Senger, Martin Hofmann-Apitius
Software Mentions: 8
Published: almost 8 years ago
10.3389/fimmu.2021.649551
TSPAN1, TMPRSS4, SDR16C5, and CTSE as Novel Panel for Pancreatic Cancer: A Bioinformatics Analysis and Experiments ValidationCited by: 11
Author(s): Yi-Jun Hua, Tiandong Li, Hua Wang, Jinyu Wu, Chuncheng Yi, Jianxiang Shi, Peng Wang, Chunhua Song, Liping Dai, Guozhong Jiang, Yuguang Huang, Yu Ye, Jitian Li
Software Mentions: 8
Published: over 4 years ago
10.1038/s41598-020-70596-9
Identification of potential diagnostic gene biomarkers in patients with osteoarthritisCited by: 13
Author(s): Xinling Wang, Yu Yang, Yong Huang, Zhu Ming-shuang, Rigao Chen, Zhanghui Liao, Shipeng Yang
Software Mentions: 8
Published: almost 5 years ago
10.3390/cancers12010045
N-Terminal Truncated Myb with New Transcriptional Activity Produced Through Use of an Alternative MYB Promoter in Salivary Gland Adenoid Cystic CarcinomaCited by: 11
Author(s): Candace A. Frerich, Hailey N. Sedam, Huining Kang, Yoshitsugu Mitani, Adel K. El‐Naggar, Scott A. Ness
Software Mentions: 8
Published: over 5 years ago
10.1002/cam4.3655
Immune landscape and a promising immune prognostic model associated with TP53 in early‐stage lung adenocarcinomaCited by: 17
Author(s): Chia-Chien Wu, Rong Xiang, Lin Wei
Software Mentions: 8
Published: over 4 years ago
10.1371/journal.pone.0127163
Genetic Deletion of the Transcriptional Repressor NFIL3 Enhances Axon Growth In Vitro but Not Axonal Repair In VivoCited by: 2
Author(s): L.R. van der Kallen, Ruben Eggers, Erich Ehlert, Joost Verhaagen, August B. Smit, Ronald E. van Kesteren
Software Mentions: 8
Published: about 10 years ago
10.1186/s13059-019-1747-7
Cell type-specific epigenetic links to schizophrenia risk in the brainCited by: 65
Author(s): Isabel Mendizabal, Stefano Berto, Noriyoshi Usui, Kazuya Toriumi, Paramita Chatterjee, Connor Douglas, Iksoo Huh, Hyeonsoo Jeong, Thomas S. Layman, Carol A. Tamminga, Todd M. Preuss, Genevieve Konopka, Soojin V. Yi
Software Mentions: 8
Published: about 6 years ago
10.1002/cam4.4156
Comprehensive analysis of a new prognosis signature based on histone deacetylases in clear cell renal cell carcinomaCited by: 6
Author(s): Fajuan Cheng, Bin Zheng, Jianwei Wang, Guiting Zhao, Zhongshun Yao, Zhihong Niu
Software Mentions: 8
Published: about 4 years ago
10.1186/s12967-021-02981-5
N6-Methyladenosine RNA modification in cerebrospinal fluid as a novel potential diagnostic biomarker for progressive multiple sclerosisCited by: 14
Author(s): Fei Ye, Tianzhu Wang, Xiaoxin Wu, Jie Liang, Jiaoxing Li, Wenli Sheng
Software Mentions: 8
Published: about 4 years ago
10.18632/oncotarget.26668
mTOR inhibition affects Yap1-β-catenin-induced hepatoblastoma growth and developmentCited by: 11
Author(s): Laura Molina, Hong Yang, Adeola O. Adebayo Michael, Michael Oertel, Aaron Bell, Sucha Singh, Xin Chen, Junyan Tao, Satdarshan P. Monga
Software Mentions: 8
Published: over 6 years ago
10.1016/j.cell.2019.08.003
Host-Microbe-Drug-Nutrient Screen Identifies Bacterial Effectors of Metformin TherapyCited by: 170
Author(s): Rosina Pryor, Povilas Norvaišas, Γεώργιος Μαρίνος, Lena Best, Louise B. Thingholm, Leonor M. Quintaneiro, Wouter De Haes, Daniela Esser, Silvio Waschina, Celia Lujan, Reuben L. Smith, Timothy A. Scott, Daniel Martínez-Martínez, Orla Woodward, Kevin Bryson, Matthias Laudes, Wolfgang Lieb, Riekelt H. Houtkooper, André Franke, Liesbet Temmerman, Ivana Bjedov, Helena M. Cochemé, Christoph Kaleta, Filipe Cabreiro
Software Mentions: 8
Published: almost 6 years ago
10.3389/fcell.2021.710207
Immunological Value of Prognostic Signature Based on Cancer Stem Cell Characteristics in Hepatocellular CarcinomaCited by: 14
Author(s): Qianhui Xu, Hao Xu, Shaohuai Chen, Wen Huang
Software Mentions: 8
Published: almost 4 years ago
10.3389/fcell.2021.642650
A Novel CpG Methylation Risk Indicator for Predicting Prognosis in Bladder CancerCited by: 9
Author(s): Yufeng Guo, Jun Yin, Yuanheng Dai, Yu-Dong Guan, Pinjin Chen, Yongqiang Chen, Chen‐Zheng Huang, Yong‐Jie Lu, Lirong Zhang, Dae‐Kyu Song
Software Mentions: 8
Published: almost 4 years ago
10.1186/s12957-021-02328-w
Identification of novel antioxidant gene signature to predict the prognosis of patients with gastric cancerCited by: 10
Author(s): Jianhua Wu, Xuan Wang, Nan Wang, Li Ma, Xin Xie, Hao Zhang, Huafeng Kang, Zhangjian Zhou
Software Mentions: 8
Published: about 4 years ago
10.1186/s12957-018-1519-y
Identification of hub genes with diagnostic values in pancreatic cancer by bioinformatics analyses and supervised learning methodsCited by: 23
Author(s): Chunyang Li, Xiaoxi Zeng, Haopeng Yu, Yuanxia Gu, Wei Zhang
Software Mentions: 8
Published: over 6 years ago
10.3390/jpm11020154
Comprehensive Profiling of Genomic and Transcriptomic Differences between Risk Groups of Lung Adenocarcinoma and Lung Squamous Cell CarcinomaCited by: 19
Author(s): Talip Zengin, Tuğba Önal-Süzek
Software Mentions: 8
Published: over 4 years ago
10.3389/fcell.2021.681745
Comprehensive Analysis of the Immune Infiltrates and PD-L1 of m6A RNA Methylation Regulators in Hepatocellular CarcinomaCited by: 9
Author(s): Yali Xu, Xueling He, Junjian Deng, Lin Xiong, Yue Li, Xiaoyu Zhang, Wenliang Chen, Xin Liu, Ximing Xu
Software Mentions: 8
Published: about 4 years ago
10.1016/j.devcel.2018.07.005
Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during DevelopmentCited by: 184
Author(s): Sueli Marques, David van Bruggen, Darya Vanichkina, Elisa M. Floriddia, Hermany Munguba, Leif Väremo, Stefania Giacomello, Ana Mendanha Falcão, Mandy Meijer, Åsa K. Björklund, Jens Hjerling-Leffler, Ryan J. Taft, Gonçalo Castelo‐Branco
Software Mentions: 8
Published: almost 7 years ago
10.1038/s41598-020-68665-0
MAF1 is a chronic repressor of RNA polymerase III transcription in the mouseCited by: 15
Author(s): Nicolas Bonhoure, Viviane Praz, Robyn D. Moir, Gilles Willemin, François Mange, Catherine Moret, Ian M. Willis, Nouria Hernandez
Software Mentions: 8
Published: about 5 years ago
10.1186/s41065-021-00201-0
Identification and validation of hub genes of synovial tissue for patients with osteoarthritis and rheumatoid arthritisCited by: 10
Author(s): Yanzhi Ge, Zuxiang Chen, Yanbin Fu, Xue Xiao, Haipeng Xu, Peijian Tong, Li Zhou
Software Mentions: 8
Published: almost 4 years ago
10.18632/oncotarget.24506
Systematic characterization of autophagy-related genes during the adipocyte differentiation using public-access dataCited by: 13
Author(s): Mahmoud Ahmed, Huynh Quoc Nguyen, Jin Seok Hwang, Sahib Zada, Trang Huyen Lai, Sang Soo Kang, Deok Ryong Kim
Software Mentions: 8
Published: over 7 years ago
10.3389/fcell.2021.712230
A Novel Ferroptosis-Related Prognostic Signature Reveals Macrophage Infiltration and EMT Status in Bladder CancerCited by: 19
Author(s): Yi‐Lin Yan, Jinming Cai, Zhengnan Huang, Xiangqian Cao, Pengyu Tang, Zeyi Wang, Fang Zhang, Shujie Xia, Bing Shen
Software Mentions: 8
Published: almost 4 years ago
10.3389/fcell.2021.653357
Combination of Immune-Related Genomic Alterations Reveals Immune Characterization and Prediction of Different Prognostic Risks in Ovarian CancerCited by: 2
Author(s): Xibo Zhao, Shanshan Cong, Qiuyan Guo, Yan Cheng, Tian Liang, Jing Wang, Guangmei Zhang
Software Mentions: 8
Published: over 4 years ago
10.1097/MD.0000000000027374
Identification and validation of a hypoxia-related prognostic signature in clear cell renal cell carcinoma patientsCited by: 7
Author(s): Zhengtian Li, Gang Du, Rong Zhao, Weibo Yang, Chan Li, Jun Huang, Zhenpei Wen, Hening Li, Bo Zhang
Software Mentions: 8
Published: almost 4 years ago
10.3389/fonc.2020.574939
Identification of an Immune-Related Gene Signature Based on Immunogenomic Landscape Analysis to Predict the Prognosis of Adult Acute Myeloid Leukemia PatientsCited by: 19
Author(s): Ruiqi Zhu, Huishan Tao, Wenyi Lin, Liang Tang, Yu Hu
Software Mentions: 8
Published: over 4 years ago
10.1242/dmm.040444
Next-generation RNA sequencing of FFPE subsections reveals highly conserved stromal reprogramming between canine and human mammary carcinomaCited by: 19
Author(s): Parisa Amini, Sina Nassiri, Julia Ettlin, Alexandra Malbon, Enni Markkanen
Software Mentions: 8
Published: over 6 years ago
10.3389/fonc.2018.00100
Genomic DNA Methylation-Derived Algorithm Enables Accurate Detection of Malignant Prostate TissuesCited by: 35
Author(s): Erfan Aref‐Eshghi, Laila C. Schenkel, Peter Ainsworth, Hanxin Lin, David I. Rodenhiser, Jean‐Claude Cutz, Bekim Sadiković
Software Mentions: 8
Published: over 7 years ago
10.7554/eLife.05005
Predicting effective microRNA target sites in mammalian mRNAsCited by: 5,158
Author(s): Vikram Agarwal, George W. Bell, Jin Wu Nam, David P. Bartel
Software Mentions: 8
Published: almost 10 years ago
10.7554/eLife.65508
Seroconversion stages COVID19 into distinct pathophysiological statesCited by: 36
Author(s): Matthew D. Galbraith, Kohl T Kinning, Kelly D. Sullivan, Ryan M. Baxter, Paula Araya, Kimberly R. Jordan, Seth Russell, Keith P Smith, Ross E Granrath, Jessica Shaw, Monika Dzieciątkowska, Tusharkanti Ghosh, Andrew A. Monte, Angelo D’Alessandro, Kirk C. Hansen, Tellen D Benett, Elena W.Y. Hsieh, Joaquín M. Espinosa
Software Mentions: 8
Published: over 4 years ago
10.1186/s13073-021-00866-2
Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epitheliumCited by: 21
Author(s): Silva Kasela, Victor E. Ortega, Molly Martorella, Suresh Garudadri, Jennifer Nguyen, Elizabeth J. Ampleford, Anu Pasanen, Srilaxmi Nerella, Kristina L. Buschur, Igor Barjaktarević, R. Graham Barr, Eugene R. Bleecker, Russell P. Bowler, Alejandro P. Comellas, Christopher B. Cooper, David Couper, Gerard J. Criner, Jeffrey L. Curtis, MeiLan K. Han, Nadia N. Hansel, Eric A. Hoffman, Robert J. Kaner, Jerry A. Krishnan, Fernando J. Martínez, Merry-Lynn McDonald, Deborah A. Meyers, Robert Paine, Stephen P. Peters, Mario Castro, Loren C. Denlinger, Serpil C. Erzurum, John V. Fahy, Elliot Israel, Nizar N. Jarjour, Bruce D. Levy, Xingnan Li, Wendy C. Moore, Sally E. Wenzel, Joe Zein, Charles Langelier, Prescott G. Woodruff, Tuuli Lappalainen, Stephanie A. Christenson
Software Mentions: 8
Published: over 4 years ago
10.3389/fonc.2020.01411
Comparison of Stage 4 and Stage 4s Neuroblastoma Identifies Autophagy-Related Gene and LncRNA Signatures Associated With PrognosisCited by: 12
Author(s): Xinyao Meng, Honglin Li, Erhu Fang, Jiexiong Feng, Xiaoli Zhao
Software Mentions: 8
Published: almost 5 years ago
10.3389/fcimb.2020.00194
Delineation and Modulation of the Natural Killer Cell Transcriptome in Rhesus Macaques During ZIKV and SIV InfectionsCited by: 2
Author(s): Malika Aïd, Daniel R. Ram, Steven E. Bosinger, Dan H. Barouch, R. Keith Reeves
Software Mentions: 8
Published: about 5 years ago
10.1016/j.csbj.2020.06.023
Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbiditiesCited by: 10
Author(s): Susan Idicula‐Thomas, Ulka Gawde, Sameeksha Bhaye, Khushal Pokar, Gary D. Bader
Software Mentions: 8
Published: over 5 years ago
10.1084/jem.20201833
ADAR and hnRNPC deficiency synergize in activating endogenous dsRNA-induced type I IFN responsesCited by: 7
Author(s): Anna‐Maria Herzner, Zia Khan, Eric L. Van Nostrand, Sara M. Chan, Trinna Cuellar, Ronald Chen, Ximo Pechuan-Jorge, László G. Kömüves, Margaret Solon, Zora Modrušan, Benjamin Haley, G Yeo, Timothy W. Behrens, Matthew L. Albert
Software Mentions: 8
Published: about 4 years ago
10.3389/fcimb.2018.00326
In Search of Biomarkers for Pathogenesis and Control of Leishmaniasis by Global Analyses of Leishmania-Infected MacrophagesCited by: 16
Author(s): Patrícia Sampaio Tavares Veras, Pablo Ivan Pereira Ramos, Juliana Perrone Bezerra de Menezes
Software Mentions: 8
Published: almost 7 years ago
10.3390/cancers13143621
HPV Infection Leaves a DNA Methylation Signature in Oropharyngeal Cancer Affecting Both Coding Genes and Transposable ElementsCited by: 10
Author(s): Diego Camuzi, Luisa Aguirre Buexm, Simone De Queiroz Chaves Lourenço, Davide Degli Esposti, Cyrille Cuenin, Monique de Souza Almeida Lopes, Francesca Manara, Fazlur Rahman Talukdar, Zdenko Herceg, Luís Felipe Ribeiro Pinto, Sheila Coelho Soares-Lima
Software Mentions: 8
Published: about 4 years ago
10.1128/mSystems.01356-20
Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral CommunitiesCited by: 26
Author(s): Jingjie Du, Ahmed A. Zayed, Kristina A. Kigerl, Kylie Zane, Matthew B. Sullivan, Phillip G. Popovich
Software Mentions: 8
Published: about 4 years ago
10.1186/s12864-017-3746-y
GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleasesCited by: 29
Author(s): Lihua Julie Zhu, Michael C. Lawrence, Ankit Gupta, Hervé Pagès, Alper Küçükural, Manuel Garber, Scot A. Wolfe
Software Mentions: 8
Published: about 8 years ago
10.1155/2020/5717498
An Integrated Autophagy-Related Long Noncoding RNA Signature as a Prognostic Biomarker for Human Endometrial Cancer: A Bioinformatics-Based ApproachCited by: 14
Author(s): Ziwei Wang, Jun Zhang, Yan Liu, Rong Zhao, Xing Zhou, Hongbo Wang
Software Mentions: 8
Published: over 4 years ago
10.3389/fonc.2020.00835
Development and Validation of a 12-Gene Immune Relevant Prognostic Signature for Lung Adenocarcinoma Through Machine Learning StrategiesCited by: 14
Author(s): Xue Li, Guoshu Bi, Cheng Zhan, Yi Zhang, Yunfeng Yuan, Hong Fan
Software Mentions: 8
Published: about 5 years ago
10.1371/journal.pone.0240824
A novel computational approach for predicting complex phenotypes in Drosophila (starvation-sensitive and sterile) by deriving their gene expression signatures from public dataCited by: 0
Author(s): Dobril Ivanov, Gerrit Bostelmann, Benoît Lan-Leung, Julie Williams, Linda Partridge, Valentina Escott‐Price, Janet M. Thornton
Software Mentions: 8
Published: almost 5 years ago
10.1038/s41598-020-62354-8
Differential stromal reprogramming in benign and malignant naturally occurring canine mammary tumours identifies disease-modulating stromal componentsCited by: 18
Author(s): Parisa Amini, Sina Nassiri, Alexandra Malbon, Enni Markkanen
Software Mentions: 8
Published: over 5 years ago
10.1016/j.immuni.2019.02.006
Anti-commensal IgG Drives Intestinal Inflammation and Type 17 Immunity in Ulcerative ColitisCited by: 121
Author(s): Tomas Castro‐Dopico, Thomas W. Dennison, John R. Ferdinand, Rebeccah J. Mathews, Aaron Fleming, Dean Clift, Benjamin J Stewart, Chenzhi Jing, Konstantina Strongili, Larisa I. Labzin, Edward J M Monk, Kourosh Saeb‐Parsy, Clare E. Bryant, Simon Clare, Miles Parkes, Menna R. Clatworthy
Software Mentions: 8
Published: over 6 years ago
10.1128/mBio.01369-21
HIV-1 Vpr Induces Widespread Transcriptomic Changes in CD4 <sup>+</sup> T Cells Early PostinfectionCited by: 6
Author(s): Hélène Bauby, Christopher Ward, Rupert Hugh-White, Chad M. Swanson, Reiner Schulz, Caroline Goujon, Michael H. Malim
Software Mentions: 8
Published: about 4 years ago
10.1038/s41598-019-48746-5
Gene Expression Predicts Histological Severity and Reveals Distinct Molecular Profiles of Nonalcoholic Fatty Liver DiseaseCited by: 93
Author(s): Stephen A. Hoang, Abdul M. Oseini, Ryan E. Feaver, Banumathi K. Cole, Amon Asgharpour, Robert Vincent, Mohammad Shadab Siddiqui, Mark Lawson, Nathan Day, Justin M. Taylor, Brian R. Wamhoff, Faridoddin Mirshahi, Melissa J. Contos, Michael O. Idowu, Arun J. Sanyal
Software Mentions: 8
Published: almost 6 years ago
10.7717/peerj.11599
A seven-lncRNA signature for predicting Ewing’s sarcomaCited by: 8
Author(s): Zhihui Chen, Xinyu Wang, Guozhu Wang, Bin Xiao, Zhe Ma, Hongliang Huo, Weiwei Li
Software Mentions: 8
Published: about 4 years ago
10.7717/peerj.10682
Identification of the hub genes in gastric cancer through weighted gene co-expression network analysisCited by: 7
Author(s): Chunyang Li, Haopeng Yu, Yajing Sun, Xiaoxi Zeng, Wei Zhang
Software Mentions: 8
Published: over 4 years ago
10.1371/journal.ppat.1009933
Trypanosoma brucei triggers a broad immune response in the adipose tissueCited by: 11
Author(s): Henrique Machado, Tiago Bizarra-Rebelo, Mariana Sequeira, Sandra Trindade, Tãnia Carvalho, Filipa Rijo‐Ferreira, Barbara Rentroia‐Pacheco, Karine Serre, Luísa M. Figueiredo
Software Mentions: 8
Published: almost 4 years ago
10.1155/2015/789516
Differential Expression Analysis in RNA-Seq by a Naive Bayes Classifier with Local NormalizationCited by: 6
Author(s): Yongchao Dou, Xiaoli Guo, Lingling Yuan, David R. Holding, Chi Zhang
Software Mentions: 8
Published: over 10 years ago
10.1038/s41597-020-00696-8
Manually curated and harmonised transcriptomics datasets of psoriasis and atopic dermatitis patientsCited by: 10
Author(s): Antonio Federico, Veera Hautanen, Nils Christian, Andreas Kremer, Angela Serra, Dario Greco
Software Mentions: 8
Published: almost 5 years ago
10.1186/s13059-019-1855-4
Common DNA sequence variation influences 3-dimensional conformation of the human genomeCited by: 66
Author(s): David U. Gorkin, Yunjiang Qiu, Ming Hu, Kipper Fletez-Brant, Tristin Liu, Anthony Schmitt, Amina Noor, Joshua Chiou, Kyle J. Gaulton, Jonathan Sebat, Yun Li, Kasper D. Hansen, Bing Ren
Software Mentions: 8
Published: over 5 years ago
10.3390/cancers13071561
NF2 and Canonical Hippo-YAP Pathway Define Distinct Tumor Subsets Characterized by Different Immune Deficiency and Treatment Implications in Human Pleural MesotheliomaCited by: 19
Author(s): Haitang Yang, Sean Hall, Beibei Sun, Liang Zhao, Yanyun Gao, Ralph A. Schmid, Swee T. Tan, Ren‐Wang Peng, Feng Yao
Software Mentions: 8
Published: over 4 years ago
10.3389/fcell.2021.704242
Two Similar Signatures for Predicting the Prognosis and Immunotherapy Efficacy of Stomach Adenocarcinoma PatientsCited by: 4
Author(s): Taohua Yue, Shuai Zuo, Jing Zhu, Shuqin Guo, Zhihao Huang, Jichang Li, Xin Wang, Yucun Liu, Shanwen Chen, Pengyuan Wang
Software Mentions: 8
Published: almost 4 years ago
10.3389/fimmu.2021.749459
A Machine Learning Model to Predict the Triple Negative Breast Cancer Immune SubtypeCited by: 24
Author(s): Zihao Chen, Maoli Wang, Rudy Leon De Wilde, Ruifa Feng, Mingqiang Su, Wenjie Shi
Software Mentions: 8
Published: almost 4 years ago
10.3389/fmed.2021.644053
Comprehensive Analysis Identifies Potential Ferroptosis-Associated mRNA Therapeutic Targets in Ovarian CancerCited by: 16
Author(s): Jiyan Zhang, Jie Xi, Ping Huang, Saitian Zeng
Software Mentions: 8
Published: over 4 years ago
10.3390/cancers13051113
MPscore: A Novel Predictive and Prognostic Scoring for Progressive MeningiomaCited by: 12
Author(s): Feili Liu, Jin Qian, Chenkai Ma
Software Mentions: 8
Published: over 4 years ago
10.1371/journal.ppat.1009602
Single cell analysis of host response to helminth infection reveals the clonal breadth, heterogeneity, and tissue-specific programming of the responding CD4+ T cell repertoireCited by: 5
Author(s): Ivy K. Brown, Nathan Dyjack, Mindy M. Miller, S. Harsha Krovi, Cydney Rios, Rachel A. Woolaver, Laura Harmacek, Ting-Hui Tu, Brian P. O’Connor, Thomas Danhorn, Brian Vestal, Laurent Gapin, Clemencia Pinilla, Max A. Seibold, James Scott‐Browne, Radleigh Santos, R. Lee Reinhardt
Software Mentions: 8
Published: about 4 years ago
10.3389/fonc.2020.590006
AUNIP Expression Is Correlated With Immune Infiltration and Is a Candidate Diagnostic and Prognostic Biomarker for Hepatocellular Carcinoma and Lung AdenocarcinomaCited by: 14
Author(s): Chenxi Ma, Wenyan Kang, Lu Yu, Zongcheng Yang, Di Tian
Software Mentions: 8
Published: over 4 years ago
10.3390/cancers11101606
A Toolbox for Functional Analysis and the Systematic Identification of Diagnostic and Prognostic Gene Expression Signatures Combining Meta-Analysis and Machine LearningCited by: 12
Author(s): Johannes A Vey, Lorenz A. Kapsner, Maximilian Fuchs, Philipp Unberath, Giulia Veronesi, Meik Kunz
Software Mentions: 8
Published: almost 6 years ago
10.1186/1471-2105-11-450
Filtering, FDR and powerCited by: 43
Author(s): Maarten van Iterson, Judith M. Boer, Renée X. de Menezes
Software Mentions: 8
Published: almost 15 years ago
10.1186/s12859-021-04166-9
PTMViz: a tool for analyzing and visualizing histone post translational modification dataCited by: 4
Author(s): Kevin Chappell, Stefan Graw, Charity L. Washam, Aaron J. Storey, Chris Bolden, Eric C. Peterson, Stephanie D. Byrum
Software Mentions: 8
Published: about 4 years ago
10.1186/s12859-018-2069-6
A gene profiling deconvolution approach to estimating immune cell composition from complex tissuesCited by: 12
Author(s): Shu Hwa Chen, Wen Yu Kuo, Sheng Su, Wei Chun Chung, Jen Ming Ho, Henry Horng Shing Lu, Chung Yen Lin
Software Mentions: 8
Published: about 7 years ago
10.3389/fendo.2020.561370
Adropin Stimulates Proliferation and Inhibits Adrenocortical Steroidogenesis in the Human Adrenal Carcinoma (HAC15) Cell LineCited by: 14
Author(s): Ewelina Stelcer, Paulina Milecka, Hanna Komarowska, Karol Jopek, Marianna Tyczewska, Marta Szyszka, Marta Leśniczak, Wiktoria Suchorska, Karlygash Bekova, Beata Szczepaniak, Marek Ruchała, Marek Karczewski, T Wierzbicki, Witold Szaflarski, Ludwik K. Malendowicz, Marcin Ruciński
Software Mentions: 8
Published: almost 5 years ago
10.1186/s12864-019-5926-4
lncDIFF: a novel quasi-likelihood method for differential expression analysis of non-coding RNACited by: 6
Author(s): Qian Li, Xiaoqing Yu, Ritu Chaudhary, Robbert J.C. Slebos, Christine H. Chung, Xuefeng Wang
Software Mentions: 8
Published: about 6 years ago
10.1155/2021/8859996
Potential Prognostic Biomarkers of Lung Adenocarcinoma Based on Bioinformatic AnalysisCited by: 17
Author(s): Jili Hou, Yong Cheng
Software Mentions: 8
Published: over 4 years ago
10.1186/1471-2105-13-222
Wavelet-based detection of transcriptional activity on a novel Staphylococcus aureus tiling microarrayCited by: 3
Author(s): Víctor Segura, Alejandro Toledo‐Arana, Maite Uzqueda, Íñigo Lasa, Arrate Muñoz-Barrutia
Software Mentions: 8
Published: almost 13 years ago
10.1371/journal.pmed.1002223
Master Regulators of Oncogenic KRAS Response in Pancreatic Cancer: An Integrative Network Biology AnalysisCited by: 38
Author(s): Shivan Sivakumar, Inês de Santiago, L Chlon, Florian Markowetz
Software Mentions: 8
Published: over 8 years ago
10.3389/fcell.2021.686664
Systematic Characterization of Novel Immune Gene Signatures Predicts Prognostic Factors in Hepatocellular CarcinomaCited by: 4
Author(s): Dafeng Xu, Yu Wang, Junzhen Wu, Yuliang Zhang, Zhehao Liu, Yonghai Chen, Jinfang Zheng
Software Mentions: 8
Published: almost 4 years ago
10.18632/aging.103475
Constructing a global transcriptional regulatory landscape for early non-small cell lung cancer to identify hub genes and key pathwaysCited by: 6
Author(s): Jianlong Bu, Pinyi Zhang, Kaibin Zhu, Yubo Yan, Bowen Shi, Junfeng Wang, Shidong Xu
Software Mentions: 8
Published: almost 5 years ago
10.3389/fonc.2021.642144
Complement C1q (C1qA, C1qB, and C1qC) May Be a Potential Prognostic Factor and an Index of Tumor Microenvironment Remodeling in OsteosarcomaCited by: 33
Author(s): Longhao Chen, Jinfu Liu, Yan Lu, Xinyu He, Chi Zhang, Huanyi Zhou
Software Mentions: 8
Published: about 4 years ago
10.1371/journal.pcbi.1008748
A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathwaysCited by: 6
Author(s): Martín Garrido‐Rodriguez, Daniel López-López, Francisco Ortuño, María Peña‐Chilet, Eduardo Muñóz, Marco A. Calzado, Joaquı́n Dopazo
Software Mentions: 8
Published: over 4 years ago
10.1371/journal.pcbi.1006378
clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasetsCited by: 45
Author(s): Davide Risso, Liam Purvis, Russell B. Fletcher, Diya Das, John Ngai, Sandrine Dudoit, Elizabeth Purdom
Software Mentions: 8
Published: almost 7 years ago
10.1186/gb-2013-14-9-r95
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq dataCited by: 594
Author(s): Franck Rapaport, Raya Khanin, Yupu Liang, Mono Pirun, Azra Krek, Paul Zumbo, Christopher E. Mason, Nicholas D. Socci, Doron Betel
Software Mentions: 8
Published: over 12 years ago
10.1186/s12859-016-1007-8
readat: An R package for reading and working with SomaLogic ADAT filesCited by: 11
Author(s): Richard Cotton, Johannes Graumann
Software Mentions: 8
Published: about 9 years ago
10.18632/aging.103947
Autophagy-related long noncoding RNAs can predict prognosis in patients with bladder cancerCited by: 11
Author(s): Cong Lai, Zhenyu Wu, Juan Shi, Kaiwen Li, Jiamin Zhu, Zhenhong Chen, Cheng Liu, Kecheng Xu
Software Mentions: 8
Published: over 4 years ago
10.3389/fonc.2020.558596
Development and Validation of Autophagy-Related Gene Signature and Nomogram for Predicting Survival in Oral Squamous Cell CarcinomaCited by: 25
Author(s): Chen Hou, Hao Cai, Yue Zhu, Shuojin Huang, Song Fan, Jinsong Hou
Software Mentions: 8
Published: almost 5 years ago
10.3389/fgene.2019.00278
Identification of Prognostic Alternative Splicing Signature in Breast CarcinomaCited by: 25
Author(s): Dong Zhang, Yi Duan, Jinjing Cun, Qifeng Yang
Software Mentions: 8
Published: over 6 years ago
10.1371/journal.pone.0248889
Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanismsCited by: 10
Author(s): Jozsef Karman, Jing Wang, Corneliu Bodea, Sherry Cao, Marc C. Levesque
Software Mentions: 8
Published: over 4 years ago
10.1186/1471-2164-12-507
Chipster: user-friendly analysis software for microarray and other high-throughput dataCited by: 294
Author(s): M Aleksi Kallio, Jarno Tuimala, Taavi Hupponen, Petri Klemelä, Massimiliano Gentile, Ilari Scheinin, M.K. Koski, Janne Käki, Eija Korpelainen
Software Mentions: 8
Published: almost 14 years ago
10.3389/fgene.2019.00624
Survival Analysis of Multi-Omics Data Identifies Potential Prognostic Markers of Pancreatic Ductal AdenocarcinomaCited by: 53
Author(s): Nitish K. Mishra, Siddesh Southekal, Chittibabu Guda
Software Mentions: 8
Published: about 6 years ago
10.18632/aging.202515
Cell differentiation trajectory predicts patient potential immunotherapy response and prognosis in gastric cancerCited by: 18
Author(s): Renshen Xiang, Yuping Rong, Yuhang Ge, Wei Song, Jun Ren, Tao Fu
Software Mentions: 8
Published: over 4 years ago
10.3389/fonc.2021.561763
Predict Colon Cancer by Pairing Plasma miRNAs: Establishment of a Normalizer-Free, Cross-Platform ModelCited by: 3
Author(s): Dashan Qin, Qingdong Guo, Rui Wei, Si Liu, Shoumin Zhu, Shutian Zhang, Li Min
Software Mentions: 8
Published: over 4 years ago
10.18632/aging.202486
Constructing a ceRNA-immunoregulatory network associated with the development and prognosis of human atherosclerosis through weighted gene co-expression network analysisCited by: 11
Author(s): Yaozhong Liu, Na Liu, Qiming Liu
Software Mentions: 8
Published: over 4 years ago
10.3389/fonc.2021.654388
MYD88 Is a Potential Prognostic Gene and Immune Signature of Tumor Microenvironment for GliomasCited by: 13
Author(s): Qinglong Guo, Xing Xiao, Jinsen Zhang
Software Mentions: 8
Published: over 4 years ago
10.1186/s12859-021-04123-6
The prognostic value of an autophagy-related lncRNA signature in hepatocellular carcinomaCited by: 19
Author(s): Shiming Yang, Yaping Zhou, Xiangxin Zhang, Lu Wang, Jianfeng Fu, Xiaotong Zhao, Yang Liu
Software Mentions: 8
Published: about 4 years ago
10.3390/jcm9092955
Optimized Identification of Advanced Chronic Kidney Disease and Absence of Kidney Disease by Combining Different Electronic Health Data Resources and by Applying Machine Learning StrategiesCited by: 8
Author(s): Christoph Weber, Lena Röschke, Luise Modersohn, Christina Lohr, Tobias Kolditz, Udo Hahn, Danny Ammon, Boris Betz, Michael Kiehntopf
Software Mentions: 8
Published: almost 5 years ago
10.1186/1471-2105-12-467
Empirical comparison of cross-platform normalization methods for gene expression dataCited by: 88
Author(s): Jason R. Rudy, Faramarz Valafar
Software Mentions: 8
Published: over 13 years ago
10.7717/peerj.12070
Prognostic impact of a lymphocyte activation-associated gene signature in GBM based on transcriptome analysisCited by: 1
Author(s): Yujia Lan, Erjie Zhao, Xinxin Zhang, Xiaojing Zhu, Linyun Wan, Aditya Suru, Yanyan Ping, Yihan Wang
Software Mentions: 8
Published: almost 4 years ago
10.1093/bib/bbv069
Gene set analysis approaches for RNA-seq data: performance evaluation and application guidelineCited by: 45
Author(s): Yasir Rahmatallah, Frank Emmert‐Streib, Galina Glazko
Software Mentions: 8
Published: almost 10 years ago
10.1186/s12859-021-04114-7
Streamlining differential exon and 3′ UTR usage with diffUTRCited by: 3
Author(s): Stefan Gerber, Gerhard Schratt, Pierre-Luc Germain
Software Mentions: 8
Published: over 4 years ago
10.18632/aging.202405
Construction and analysis of a joint diagnosis model of random forest and artificial neural network for heart failureCited by: 25
Author(s): Yuqing Tian, Jiefu Yang, Ming Lan, Tong Zou
Software Mentions: 8
Published: over 4 years ago