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: limma

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

Linear Models for Microarray Data
3 versions
Latest release: about 1 year ago
314 dependent packages
4,663,292 downloads total

Papers Mentioning limma 7,776

10.1038/s41598-021-97362-9
N6-methylandenosine-related lncRNAs play an important role in the prognosis and immune microenvironment of pancreatic ductal adenocarcinoma
Cited by: 5
Author(s): Yuhai Hu, Yiping Chen
Software Mentions: 14
Published: about 3 years ago
10.1186/s12967-021-02952-w
Molecular subtype identification and prognosis stratification by a metabolism-related gene expression signature in colorectal cancer
Cited by: 20
Author(s): Daowei Lin, Wenhua Fan, Rongxin Zhang, Enen Zhao, Pansong Li, Wenhao Zhou, Jianhong Peng, Liren Li
Software Mentions: 14
Published: over 3 years ago
10.1111/jcmm.15705
Collagen Type III Alpha 1 chain regulated by GATA‐Binding Protein 6 affects Type II IFN response and propanoate metabolism in the recurrence of lower grade glioma
Cited by: 18
Author(s): Runzhi Huang, Zhenyu Li, Xiaolong Zhu, Penghui Yan, Dianwen Song, Huabin Yin, Peng Hu, Ruoyi Lin, Shengyu Wu, Tong Meng, Jie Zhang, Zongqiang Huang
Software Mentions: 14
Published: over 4 years ago
10.1371/journal.pcbi.1003000
Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq
Cited by: 55
Author(s): Oscar Franzén, Jon Jerlström-Hultqvist, Elin Einarsson, Johan Ankarklev, Marcela Ferella, Björn Andersson, Staffan G. Svärd
Software Mentions: 13
Published: over 11 years ago
10.12688/f1000research.8986.2
Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses
Cited by: 483
Author(s): Ben J. Callahan, Kris Sankaran, Julia Fukuyama, Paul J. McMurdie, Susan Holmes
Software Mentions: 13
Published: about 8 years ago
10.3389/fbioe.2020.00515
Construction of a Competitive Endogenous RNA Network for Pancreatic Adenocarcinoma Based on Weighted Gene Co-expression Network Analysis and a Prognosis Model
Cited by: 4
Author(s): Jing Wang, Jinzhu Xiang, Xueling Li
Software Mentions: 13
Published: over 4 years ago
10.1186/s12967-021-02889-0
Pan-cancer characterization of metabolism-related biomarkers identifies potential therapeutic targets
Cited by: 6
Author(s): Guoshu Bi, Yunyi Bian, Jiaqi Liang, Jiacheng Yin, Runmei Li, Mengnan Zhao, Yiwei Huang, Tao Lu, Cheng Zhan, Hong Fan, Qun Wang
Software Mentions: 13
Published: over 3 years ago
10.3389/fgene.2020.00620
An Analysis Regarding the Association Between the ISLR Gene and Gastric Carcinogenesis
Cited by: 13
Author(s): Shu Li, Wei Zhao, Manyi Sun
Software Mentions: 13
Published: over 4 years ago
10.3389/fimmu.2019.02887
Meta-Analysis of in vitro-Differentiated Macrophages Identifies Transcriptomic Signatures That Classify Disease Macrophages in vivo
Cited by: 29
Author(s): Hung Jen Chen, Andrew Y. Li Yim, Guillermo R. Griffith, Wouter J. de Jonge, Marcel M.A.M. Mannens, Enrico Ferrero, Peter Henneman, Menno P.J. de Winther
Software Mentions: 13
Published: almost 5 years ago
10.3389/fimmu.2021.730346
Nasal Immunization With Small Molecule Mast Cell Activators Enhance Immunity to Co-Administered Subunit Immunogens
Cited by: 6
Author(s): Brandi T. Johnson‐Weaver, Hae Woong Choi, Hui Yang, Joshua A. Granek, Cliburn Chan, Soman N. Abraham, Herman F. Staats
Software Mentions: 13
Published: about 3 years ago
10.3389/fonc.2020.629909
Identification of an Immune Gene-Associated Prognostic Signature and Its Association With a Poor Prognosis in Gastric Cancer Patients
Cited by: 15
Author(s): Xiaoqing Guan, Zhiyuan Xu, Runzhe Chen, Jiang‐Jiang Qin, Xiangdong Cheng
Software Mentions: 13
Published: almost 4 years ago
10.3389/fonc.2021.623170
Clinical and Prognostic Pan-Cancer Analysis of N6-Methyladenosine Regulators in Two Types of Hematological Malignancies: A Retrospective Study Based on TCGA and GTEx Databases
Cited by: 21
Author(s): Xiangsheng Zhang, Li-Ye Zhong, Zhilin Zou, Guosheng Liang, Zhenye Tang, Kai Li, Shuhua Tan, Yongmei Huang, Xiao Zhu
Software Mentions: 13
Published: over 3 years ago
10.3389/fonc.2021.697948
Development and Validation of a Nomogram and a Comprehensive Prognostic Analysis of an LncRNA-Associated Competitive Endogenous RNA Network Based on Immune-Related Genes for Locally Advanced Rectal Cancer With Neoadjuvant Therapy
Cited by: 2
Author(s): Fang-Ze Wei, Shiwen Mei, Zhijie Wang, Jianan Chen, Huan Shen, Fen Zhao, Juan Li, Tixian Xiao, Qian Liu
Software Mentions: 13
Published: over 3 years ago
10.12688/f1000research.8967.2
An end to end workflow for differential gene expression using Affymetrix microarrays
Cited by: 16
Author(s): Bernd Klaus, Stefanie Reisenauer
Software Mentions: 13
Published: over 6 years ago
10.3389/fmolb.2021.689224
Immune-Related lncRNA Signature for Predicting the Immune Landscape of Head and Neck Squamous Cell Carcinoma
Cited by: 13
Author(s): Yin Ji, Xiaohui Li, Caifeng Lv, Xian He, Xiaoqin Luo, Sen Li, Wenjian Hu
Software Mentions: 13
Published: over 3 years ago
10.3390/cancers13174311
Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging
Cited by: 15
Author(s): Daria Lazic, Florian Kromp, Fikret Rifatbegovic, Peter Repiščák, Michael Kirr, Filip Mívalt, Florian Halbritter, Marie Bernkopf, Andrea Bileck, Marek Ussowicz, Inge M. Ambros, Peter F. Ambros, Christopher Gerner, Ruth Ladenstein, Christian Ostalecki, Sabine Taschner‐Mandl
Software Mentions: 13
Published: about 3 years ago
10.1371/journal.pone.0212669
Batch adjustment by reference alignment (BARA): Improved prediction performance in biological test sets with batch effects
Cited by: 3
Author(s): Robin Gradin, Malin Lindstedt, Henrik J. Johansson
Software Mentions: 13
Published: over 5 years ago
10.3389/fneur.2020.579683
Development and Validation of a Five-Gene Signature to Predict Relapse-Free Survival in Multiple Sclerosis
Cited by: 6
Author(s): Fei Ye, Jie Liang, Jiaoxing Li, Haiyan Li, Wenli Sheng
Software Mentions: 13
Published: almost 4 years ago
10.7554/eLife.07836
Lipid-mediated regulation of SKN-1/Nrf in response to germ cell absence
Cited by: 158
Author(s): Michael J. Steinbaugh, Sri Devi Narasimhan, Stacey Robida-Stubbs, Lorenza E Moronetti Mazzeo, Jonathan M. Dreyfuss, John M. Hourihan, Prashant Raghavan, Theresa N. Operaña, Reza Esmaillie, T. Keith Blackwell
Software Mentions: 13
Published: about 9 years ago
10.7554/eLife.50087
Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle
Cited by: 58
Author(s): Elias T Friman, Cédric Deluz, Antonio C. A. Meireles-Filho, Subashika Govindan, Vincent Gardeux, Bart Deplancke, David M. Suter
Software Mentions: 13
Published: almost 5 years ago
10.1038/srep42130
Dissecting the brown adipogenic regulatory network using integrative genomics
Cited by: 20
Author(s): Rachana Pradhan, Johannes Bues, Vincent Gardeux, Petra Schwalie, Daniel Alpern, Wanze Chen, Julie Russeil, Sunil K. Raghav, Bart Deplancke
Software Mentions: 13
Published: almost 8 years ago
10.3390/cancers11010091
The Potential Mechanism of Bufadienolide-Like Chemicals on Breast Cancer via Bioinformatics Analysis
Cited by: 5
Author(s): Yingbo Zhang, Xiaomin Tang, Yuxin Pang, Luqi Huang, Dan Wang, Chao Yuan, Xuan Hu, Liping Qu
Software Mentions: 13
Published: almost 6 years ago
10.1099/mgen.0.000492
Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes
Cited by: 13
Author(s): Chun Shen Lim, Vitina Sozzi, Margaret Littlejohn, Lilly Yuen, Nadia Warner, Brigid Betz‐Stablein, Fabio Luciani, Peter Revill, Chris M. Brown
Software Mentions: 13
Published: almost 4 years ago
10.3389/fgene.2021.652189
Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance
Cited by: 11
Author(s): Chirag Gupta, Venkategowda Ramegowda, Supratim Basu, Andy Pereira
Software Mentions: 13
Published: over 3 years ago
10.3389/fgene.2021.690530
Predicting the Survival and Immune Landscape of Colorectal Cancer Patients Using an Immune-Related lncRNA Pair Model
Cited by: 3
Author(s): Chi Ma, Xin Zhang, Xudong Zhao, Nan Zhang, Sixin Zhou, Yonghui Zhang, Peiyu Li
Software Mentions: 13
Published: about 3 years ago
10.1186/s13059-020-02151-8
Alignment and mapping methodology influence transcript abundance estimation
Cited by: 80
Author(s): Avi Srivastava, Laraib Malik, Hirak Sarkar, Mohsen Zakeri, Fatemeh Almodaresi, Charlotte Soneson, Michael I. Love, Carl Kingsford, Rob Patro
Software Mentions: 13
Published: about 4 years ago
10.1186/s12859-019-3251-1
BISR-RNAseq: an efficient and scalable RNAseq analysis workflow with interactive report generation
Cited by: 17
Author(s): Venkat Sundar Gadepalli, Hatice Gülçin Özer, Ayse Selen Yilmaz, Maciej Pietrzak, Amy Webb
Software Mentions: 13
Published: almost 5 years ago
10.1186/1471-2164-14-46
Systems infection biology: a compartmentalized immune network of pig spleen challenged with Haemophilus parasuis
Cited by: 9
Author(s): Ming Zhao, Xiangdong Liu, Xinyun Li, Hongbo Chen, Hui Jin, Rui Zhou, Mengjin Zhu, Shuhong Zhao
Software Mentions: 13
Published: almost 12 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/s12885-020-07695-3
Comprehensive analysis of prognostic gene signatures based on immune infiltration of ovarian cancer
Cited by: 18
Author(s): Shi-Bai Yan, Jinling Fang, Yongcai Chen, Yong Xie, Siyou Zhang, Xiaohui Zhu, Fang Fěng
Software Mentions: 13
Published: almost 4 years ago
10.1186/s12859-021-04268-4
A comprehensive database for integrated analysis of omics data in autoimmune diseases
Cited by: 10
Author(s): Jordi Martorell-Marugán, Raúl López-Domínguez, Adrián García-Moreno, Daniel Toro-Domínguez, Juan Antonio Villatoro-García, Guillermo Barturen, Adoración Martín-Gómez, Kevin Troulé, Gonzalo Gómez‐López, Fátima Al‐Shahrour, Víctor González‐Rumayor, María Peña‐Chilet, Joaquín Dopazo, Julio Sáez-Rodríguez, Marta E. Alarcón‐Riquelme, Pedro Carmona-Sáez
Software Mentions: 13
Published: over 3 years ago
10.1186/1748-7188-4-7
Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity
Cited by: 71
Author(s): Koji Kadota, Yuji Nakai, Kentaro Shimizu
Software Mentions: 13
Published: over 15 years ago
10.1186/s12859-021-04142-3
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses
Cited by: 11
Author(s): Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise A Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordóñez, Andrew E. Jaffe, Leonardo Collado‐Torres
Software Mentions: 13
Published: over 3 years ago
10.1186/s12859-015-0794-7
Evaluation of methods for differential expression analysis on multi-group RNA-seq count data
Cited by: 47
Author(s): Min Tang, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 13
Published: about 9 years ago
10.3389/fonc.2021.678694
A Novel Ferroptosis-Related Pathway for Regulating Immune Checkpoints in Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Su Gao, Hailong Ruan, Jingchong Liu, Yuenan Liu, Di Liu, Junwei Tong, Jian Shi, Hongmei Yang, Tianbo Xu, Xiaoping Zhang
Software Mentions: 13
Published: over 3 years ago
10.1093/bioinformatics/bty713
Bigmelon: tools for analysing large DNA methylation datasets
Cited by: 47
Author(s): T.J. Gorrie-Stone, Melissa Smart, Ayden Saffari, Karim Malki, Eilís Hannon, Joe Burrage, Jonathan Mill, Meena Kumari, Leonard C Schalkwyk
Software Mentions: 13
Published: about 6 years ago
10.1093/bib/bbz158
Toward a gold standard for benchmarking gene set enrichment analysis
Cited by: 74
Author(s): Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity W. Law, Sean Davis, Vincent J. Carey, Martin Morgan, Ralf Zimmer, Levi Waldron
Software Mentions: 13
Published: over 4 years ago
10.1186/s12859-016-1457-z
Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq
Cited by: 55
Author(s): Claire Williams, Alyssa Baccarella, Jay Z. Parrish, Charles C. Kim
Software Mentions: 13
Published: almost 8 years ago
10.1186/s12864-021-07542-0
Variation of microRNA expression in the human placenta driven by population identity and sex of the newborn
Cited by: 8
Author(s): Songlin Guo, Shouxiong Huang, Xi Jiang, Haiyang Hu, Dingding Han, Carlos S. Moreno, Genevieve Fairbrother, David A. Hughes, Mark Stoneking, Philipp Khaitovich
Software Mentions: 13
Published: over 3 years ago
10.3389/fcimb.2021.688256
Machine Learning Uses Chemo-Transcriptomic Profiles to Stratify Antimalarial Compounds With Similar Mode of Action
Cited by: 1
Author(s): Ashleigh van Heerden, Roelof van Wyk, Lyn-Marié Birkholtz
Software Mentions: 13
Published: over 3 years ago
10.1186/s12859-019-3029-5
CAGEfightR: analysis of 5′-end data using R/Bioconductor
Cited by: 35
Author(s): Malte Thodberg, Axel Thieffry, Kristoffer Vitting-Seerup, Robin Andersson, Albin Sandelin
Software Mentions: 13
Published: about 5 years ago
10.1038/s41598-018-19655-w
msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data
Cited by: 10
Author(s): Benjamin Mayne, Shalem Leemaqz, Sam Buckberry, Carlos M. Rodríguez López, Claire T. Roberts, Tina Bianco‐Miotto, James Breen
Software Mentions: 12
Published: almost 7 years ago
10.1111/jcmm.16605
Leptin receptor is a key gene involved in the immunopathogenesis of thyroid‐associated ophthalmopathy
Cited by: 3
Author(s): Ziyi Chen, Zhe Chen, Jingya Wang, Meng Zhang, Xiaofei Wang, Deji Cuomu, Bingyin Shi, Yue Wang
Software Mentions: 12
Published: over 3 years ago
10.1186/1471-2105-11-194
Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data
Cited by: 32
Author(s): Benedikt Zacher, Pei Fen Kuan, Achim Tresch
Software Mentions: 12
Published: over 14 years ago
10.3389/fonc.2021.625207
MYCN Drives a Tumor Immunosuppressive Environment Which Impacts Survival in Neuroblastoma
Cited by: 18
Author(s): Salvatore Raieli, Daniele Di Renzo, Silvia Lampis, Camilla Amadesi, Luca Montemurro, Andrea Pession, Patrizia Hrelia, Matthias Fischer, Roberto Tonelli
Software Mentions: 12
Published: over 3 years ago
10.1186/s12859-015-0763-1
ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data
Cited by: 29
Author(s): Ivana Ihnatová, Eva Budínská
Software Mentions: 12
Published: about 9 years ago
10.3390/genes12030352
Temporal Dynamic Methods for Bulk RNA-Seq Time Series Data
Cited by: 10
Author(s): Vera-Khlara S. Oh, Robert W. Li
Software Mentions: 12
Published: over 3 years ago
10.1155/2021/5575286
Screening and Bioinformatics Analysis of Competitive Endogenous RNA Regulatory Network ––Related to Circular RNA in Breast Cancer
Cited by: 3
Author(s): Tao Wang, Yi Zhang, Yan He, Yang Liu, Qi Peng
Software Mentions: 12
Published: about 3 years ago
10.1038/s42003-019-0415-5
diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering
Cited by: 137
Author(s): Lukas M. Weber, Małgorzata Nowicka, Charlotte Soneson, Mark D. Robinson
Software Mentions: 12
Published: over 5 years ago
10.18632/aging.202871
A novel focal adhesion related gene signature for prognostic prediction in hepatocellular carcinoma
Cited by: 4
Author(s): Zhuo Lin, Dan Miao, Xu Qian, Xiaodong Wang, Fang Yu
Software Mentions: 12
Published: over 3 years ago
10.1007/s00401-020-02226-7
Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology
Cited by: 69
Author(s): Anna Golebiewska, Ann-Christin Hau, Anaïs Oudin, Daniel Stieber, Yahaya A Yabo, Virginie Baus, Vanessa Barthelemy, Eliane Klein, Sébastien Bougnaud, Olivier Keunen, May Wantz, Alessandro Michelucci, Virginie Neirinckx, Arnaud Muller, Tony Kaoma, Petr V. Nazarov, Francisco Azuaje, Alfonso De Falco, Ben Flies, Lorraine Richart, Suresh Poovathingal, Thaís Arns, Kamil Grzyb, Andreas Möck, Christel Herold‐Mende, Anne Steinø, Dennis Brown, Patrick May, Hrvoje Miletić, Tathiane M. Malta, Houtan Noushmehr, Yong-Jun Kwon, Winnie Jahn, Barbara Klink, Georgette Tanner, Lucy F. Stead, Michel Mittelbronn, Alexander Skupin, Frank Hutter, Rolf Bjerkvig, Simone P. Niclou
Software Mentions: 12
Published: about 4 years ago
10.3389/fimmu.2020.01659
Conventional and Computational Flow Cytometry Analyses Reveal Sustained Human Intrathymic T Cell Development From Birth Until Puberty
Cited by: 2
Author(s): Marieke Lavaert, Brecht Valcke, Bart Vandekerckhove, Georges Leclercq, Kai Ling Liang, Tom Taghon
Software Mentions: 12
Published: over 4 years ago
10.3389/fimmu.2021.698236
Comprehensive Analysis of Clinical Significance, Immune Infiltration and Biological Role of m6A Regulators in Early-Stage Lung Adenocarcinoma
Cited by: 3
Author(s): Bolun Zhou, Shugeng Gao
Software Mentions: 12
Published: about 3 years ago
10.1186/s12935-021-01900-4
Role of tumor mutation burden-related signatures in the prognosis and immune microenvironment of pancreatic ductal adenocarcinoma
Cited by: 16
Author(s): Rong Tang, Xiaomeng Liu, Wei Wang, Jie Hua, Jin Xu, Chen Liang, Qingcai Meng, Jiang Liu, Bo Zhang, Yu Lei, Si Shi
Software Mentions: 12
Published: over 3 years ago
10.18632/aging.202317
Identification and validation of an immune-related gene signature predictive of overall survival in colon cancer
Cited by: 33
Author(s): Xuening Zhang, Hao Zhao, Xiaoguang Shi, Xiaocan Jia, Yongli Yang
Software Mentions: 12
Published: almost 4 years ago
10.1371/journal.pone.0079217
A Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and Specificity
Cited by: 154
Author(s): Adi L. Tarca, Gaurav Bhatti, Roberto Romero
Software Mentions: 12
Published: about 11 years ago
10.1155/2021/4743971
Exploration of the Immune-Related Signatures and Immune Infiltration Analysis in Melanoma
Cited by: 0
Author(s): Ai-lan Li, Yong‐Mei Zhu, Lai-qiang Gao, Shuyue Wei, Mingtao Wang, Qiang Ma, Yuanna Zheng, Jianhua Li, Qingfeng Wang
Software Mentions: 12
Published: almost 4 years ago
10.3389/fcimb.2021.687607
Early Leukocyte Responses in Ex-Vivo Models of Healing and Non-Healing Human Leishmania (Viannia) panamensis Infections
Cited by: 1
Author(s): María Adelaida Gómez, Ashton T. Belew, Adriana Navas, Mariana Rosales-Chilama, Julieth Murillo, Laura A. L. Dillon, Theresa A Alexander, Álvaro José Martínez-Valencia, Najib M. El-Sayed
Software Mentions: 12
Published: about 3 years ago
10.3389/fimmu.2021.647832
Large-Scale Gene Expression Signatures Reveal a Microbicidal Pattern of Activation in Mycobacterium leprae-Infected Monocyte-Derived Macrophages With Low Multiplicity of Infection
Cited by: 9
Author(s): Thyago Leal-Calvo, Bruna Letícia Martins, Daniele Ferreira de Faria Bertoluci, Patrícia Sammarco Rosa, Rodrigo Mendes de Camargo, G. Germano, Vânia Niéto Brito de Souza, Ana Carla Pereira Latini, Milton Ozório Moraes
Software Mentions: 12
Published: over 3 years ago
10.1186/s12957-021-02175-9
A prognostic model for hepatocellular carcinoma based on apoptosis-related genes
Cited by: 15
Author(s): Renjie Liu, Guifu Wang, Chi Zhang, Dou‐Sheng Bai
Software Mentions: 12
Published: over 3 years ago
10.7717/peerj.10255
Comprehensive genomic analysis of microenvironment phenotypes in ovarian cancer
Cited by: 4
Author(s): Jingshu Wang, Tingting Zhang, Lina Yang, Gong Yang
Software Mentions: 12
Published: almost 4 years ago
10.1002/cam4.4092
Gene signatures predict biochemical recurrence‐free survival in primary prostate cancer patients after radical therapy
Cited by: 6
Author(s): Qiang Su, Zhenyu Liu, Chi Chen, Han Gao, Yongbei Zhu, Liusu Wang, Meiqing Pan, Jiangang Liu, Xin Yang, Jie Tian
Software Mentions: 12
Published: about 3 years ago
10.3389/fonc.2021.654076
A Novel Ferroptosis Related Gene Signature for Prognosis Prediction in Patients With Colon Cancer
Cited by: 29
Author(s): Jianhua Nie, Dan Shan, Shun Li, Shuyuan Zhang, Xiaolin Zi, Fan Xing, Jiaqi Shi, Caiqi Liu, Tianjiao Wang, Xiankai Sun, Qian Zhang, Meng Zhou, Sai Luo, Hongxue Meng, Yanqiao Zhang, Tongsen Zheng
Software Mentions: 12
Published: over 3 years ago
10.1371/journal.pone.0190152
RNA-Seq differential expression analysis: An extended review and a software tool
Cited by: 389
Author(s): Juliana Costa-Silva, Douglas Silva Domingues, Fabrício Martins Lopes
Software Mentions: 12
Published: almost 7 years ago
10.7717/peerj.9847
Prognostic implications of metabolism-associated gene signatures in colorectal cancer
Cited by: 21
Author(s): Yifei Miao, Qiutian Li, Jiangtao Wang, Wuxia Quan, Chen Li, Yuan Yang, Denghai Mi
Software Mentions: 12
Published: about 4 years ago
10.3389/fphar.2021.726529
CD3D, GZMK, and KLRB1 Are Potential Markers for Early Diagnosis of Rheumatoid Arthritis, Especially in Anti-Citrullinated Protein Antibody-Negative Patients
Cited by: 8
Author(s): Junqin Lu, Yihui Bi, Yapeng Zhu, Hanyu Shi, Wenxiu Duan, Jian Zhou
Software Mentions: 12
Published: about 3 years ago
10.7717/peerj.10469
BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis
Cited by: 5
Author(s): Daniel Dimitrov, Quan Gu
Software Mentions: 12
Published: almost 4 years ago
10.12688/f1000research.12544.1
Easy and efficient ensemble gene set testing with EGSEA
Cited by: 45
Author(s): Monther Alhamdoosh, Charity W. Law, Tian Li, Julie Sheridan, Milica Ng, Matthew E. Ritchie
Software Mentions: 12
Published: about 7 years ago
10.1038/srep18871
LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights
Cited by: 37
Author(s): Xinran Dong, Yun Huang, Xiao Wang, Weidong Tian
Software Mentions: 12
Published: almost 9 years ago
10.12688/f1000research.27893.1
A guide to creating design matrices for gene expression experiments
Cited by: 18
Author(s): Charity W. Law, Kathleen Zeglinski, Xueyi Dong, Monther Alhamdoosh, Gordon K. Smyth, Matthew E. Ritchie
Software Mentions: 12
Published: almost 4 years ago
10.1186/s12967-021-02800-x
Identification of 4 immune cells and a 5-lncRNA risk signature with prognosis for early-stage lung adenocarcinoma
Cited by: 25
Author(s): Liancai Mu, Ke Ding, Ranran Tu, Wei Yang
Software Mentions: 12
Published: over 3 years ago
10.12688/f1000research.8839.3
A cross-package Bioconductor workflow for analysing methylation array data
Cited by: 80
Author(s): Jovana Maksimovic, Belinda Phipson, Alicia Oshlack
Software Mentions: 12
Published: over 7 years ago
10.3389/fonc.2019.01361
Development and Validation of an RNA-Seq-Based Prognostic Signature in Neuroblastoma
Cited by: 28
Author(s): Jianguo Zhou, Bo Liang, Sanli Jin, Hui-Ling Liao, Guocheng Du, Long Cheng, Hu Ma, Udo S. Gaipl
Software Mentions: 12
Published: almost 5 years ago
10.12688/f1000research.24187.2
ExploreModelMatrix: Interactive exploration for improved understanding of design matrices and linear models in R
Cited by: 0
Author(s): Charlotte Soneson, Fédérico Marini, Florian Geier, Michael I. Love, Michael Stadler
Software Mentions: 12
Published: about 4 years ago
10.12688/f1000research.17082.2
Correction of gene model annotations improves isoform abundance estimates: the example of ketohexokinase (Khk)
Cited by: 4
Author(s): Christophe D. Chabbert, Tanja Eberhart, Ilaria Guccini, Wilhelm Krek, Werner J. Kovacs
Software Mentions: 12
Published: over 5 years ago
10.1002/cam4.4126
Hypoxia‐related lncRNAs to build prognostic classifier and reveal the immune characteristics of EGFR wild type and low expression of PD‐L1 squamous and adenocarcinoma NSCLC
Cited by: 4
Author(s): Fang Zhao, Min Wang, Jie Zhu
Software Mentions: 12
Published: over 3 years ago
10.1007/s12032-017-0963-9
The identification of key genes and pathways in hepatocellular carcinoma by bioinformatics analysis of high-throughput data
Cited by: 107
Author(s): Chaoyang Zhang, Li Peng, Yaqin Zhang, Zhaoyang Liu, Wenling Li, Shilian Chen, Guancheng Li
Software Mentions: 12
Published: over 7 years ago
10.3389/fgene.2021.687778
Pan-Cancer Analysis of PIMREG as a Biomarker for the Prognostic and Immunological Role
Cited by: 16
Author(s): Hua Zhu, Xinyao Hu, Yingze Ye, Zhihong Jian, Yi Zhong, Lijuan Gu, Xiaoxing Xiong
Software Mentions: 12
Published: about 3 years ago
10.3389/fgene.2020.00906
Construction and Validation of Novel Diagnostic and Prognostic DNA Methylation Signatures for Hepatocellular Carcinoma
Cited by: 7
Author(s): Ran Li, Liyan Shui, Junling Jia, Chao Wu
Software Mentions: 12
Published: over 4 years ago
10.12688/f1000research.9501.2
A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
Cited by: 693
Author(s): Aaron T. L. Lun, Davis J. McCarthy, John C. Marioni
Software Mentions: 12
Published: about 8 years ago
10.1371/journal.pone.0075146
NuChart: An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations
Cited by: 29
Author(s): Ivan Merelli, Píetro Lió, Luciano Milanesi
Software Mentions: 12
Published: about 11 years ago
10.7554/eLife.58993
Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns
Cited by: 23
Author(s): Kathleen Greenham, Ryan C. Sartor, Stevan Zorich, Ping Lou, Todd C. Mockler, C. Robertson McClung
Software Mentions: 12
Published: about 4 years ago
10.1038/srep26451
Glycosyltransferase Gene Expression Profiles Classify Cancer Types and Propose Prognostic Subtypes
Cited by: 52
Author(s): Jahanshah Ashkani, Kevin J. Naidoo
Software Mentions: 12
Published: over 8 years ago
10.3389/fmolb.2021.681526
Identification of Key Biomarkers and Immune Infiltration in Systemic Juvenile Idiopathic Arthritis by Integrated Bioinformatic Analysis
Cited by: 2
Author(s): Min Zhang, Rongxin Dai, Qianqian Zhao, Lina Zhou, Yunfei An, Xuemei Tang, Xiaodong Zhao
Software Mentions: 12
Published: over 3 years ago
10.3389/fgene.2020.00968
Systematic Transcriptome Analysis of Noise-Induced Hearing Loss Pathogenesis Suggests Inflammatory Activities and Multiple Susceptible Molecules and Pathways
Cited by: 6
Author(s): Quan Wang, Yilin Shen, Hongbo Hu, Fan Cui, Andi Zhang, Rui Ding, Bin Ye, Ming Xiang
Software Mentions: 12
Published: about 4 years ago
10.1038/s41598-021-86286-z
Construction and validation of a metabolic risk model predicting prognosis of colon cancer
Cited by: 5
Author(s): Didi Zuo, Chao Li, Tao Liu, Meng Yue, Jiantao Zhang, Guang Ning
Software Mentions: 12
Published: over 3 years ago
10.3390/cancers12030692
Hypoxia-Induced Adaptations of miRNomes and Proteomes in Melanoma Cells and Their Secreted Extracellular Vesicles
Cited by: 29
Author(s): Geoffroy Walbrecq, Odile Lecha, Anthoula Gaigneaux, Miriam Rebecca Fougeras, Demetra Philippidou, Christiane Margue, Miléne Tetsi Nomigni, François Bernardin, Gunnar Dittmar, Iris Behrmann, Stephanie Kreis
Software Mentions: 11
Published: over 4 years ago
10.3389/fgene.2021.620705
Identification of Tumor Microenvironment-Related Prognostic Genes in Sarcoma
Cited by: 6
Author(s): Dongjun Dai, Lanyu Xie, Yongjie Shui, Jinfan Li, Qichun Wei
Software Mentions: 11
Published: almost 4 years ago
10.7554/eLife.58705
Co-expression analysis reveals interpretable gene modules controlled by trans-acting genetic variants
Cited by: 23
Author(s): Liis Kolberg, Nurlan Kerimov, Hedi Peterson, Kaur Alasoo
Software Mentions: 11
Published: about 4 years ago
10.1186/s13058-021-01451-6
Transcriptome and genome evolution during HER2-amplified breast neoplasia
Cited by: 3
Author(s): Peipei Lu, Joseph W. Foley, Chunfang Zhu, Katherine McNamara, Korsuk Sirinukunwattana, Sujay Vennam, Sushama Varma, Hamid Fehri, Arunima Srivastava, Shirley Zhu, Jens Rittscher, Parag Mallick, Christina Curtis, Robert B. West
Software Mentions: 11
Published: over 3 years ago
10.3389/fmolb.2021.559800
KIF18B is a Prognostic Biomarker and Correlates with Immune Infiltrates in Pan-Cancer
Cited by: 9
Author(s): Mengjun Qiu, Qiushuang Wang, Qiuting Li, Lisheng Zhu, Yanan Li, Shengli Yang, Zhifan Xiong
Software Mentions: 11
Published: over 3 years ago
10.3389/fmolb.2021.684050
Characterization of Hypoxia-Related Molecular Subtypes in Clear Cell Renal Cell Carcinoma to Aid Immunotherapy and Targeted Therapy via Multi-Omics Analysis
Cited by: 10
Author(s): Weimin Zhong, Hongbin Zhong, Fengling Zhang, Chaoqun Huang, Yao Lin, Jian Huang
Software Mentions: 11
Published: over 3 years ago
10.1038/s41598-021-88698-3
In-depth transcriptomic analysis of human retina reveals molecular mechanisms underlying diabetic retinopathy
Cited by: 23
Author(s): Kolja Becker, H. Klein, Eric J. Simon, Coralie Viollet, Christian Haslinger, Germán Leparc, Christian Schultheis, Victor Chong, Markus H. Kuehn, Francesc Fernández-Albert, Remko A. Bakker
Software Mentions: 11
Published: over 3 years ago
10.3390/cancers13122903
Integrative Transcriptomic Analysis Reveals Distinctive Molecular Traits and Novel Subtypes of Collecting Duct Carcinoma
Cited by: 6
Author(s): Chiara Gargiuli, Pierangela Sepe, Anna Tessari, Tyler Sheetz, Maurizio Colecchia, F.G.M. De Braud, Giuseppe Procopio, Marialuisa Sensi, Elena Verzoni, Matteo Dugo
Software Mentions: 11
Published: over 3 years ago
10.1371/journal.pone.0188873
A comprehensive analysis of breast cancer microbiota and host gene expression
Cited by: 105
Author(s): Kevin J. Thompson, James N. Ingle, Xiaojia Tang, Nicholas Chia, Patricio Jeraldo, Marina Walther-Antonio, Karunya K. Kandimalla, Stephen Johnson, Jingwen Yao, Sean C. Harrington, Vera J. Suman, Liewei Wang, Richard Weinshilboum, Judy C. Boughey, Jean Pierre A. Kocher, Heidi Nelson, Matthew P. Goetz, Krishna R. Kalari
Software Mentions: 11
Published: almost 7 years ago
10.3389/fmolb.2021.611508
CXCL10 is a Tumor Microenvironment and Immune Infiltration Related Prognostic Biomarker in Pancreatic Adenocarcinoma
Cited by: 17
Author(s): Huimin Huang, Wangxiao Zhou, Renpin Chen, Bingfeng Xiang, Shipeng Zhou, Linhua Lan
Software Mentions: 11
Published: almost 4 years ago
10.1016/j.ebiom.2018.04.010
Genomic Response to Vitamin D Supplementation in the Setting of a Randomized, Placebo-Controlled Trial
Cited by: 28
Author(s): Antonio J. Berlanga‐Taylor, Katharine Plant, Andrew Dahl, Evelyn Lau, Michael Hill, David Sims, Andreas Heger, Jonathan Emberson, Jane Armitage, Robert Clarke, Julian C. Knight
Software Mentions: 11
Published: over 6 years ago
10.3389/fgene.2015.00040
Integrating multi-omic features exploiting Chromosome Conformation Capture data
Cited by: 9
Author(s): Ivan Merelli, Fabio Tordini, Maurizio Drocco, Marco Aldinucci, Píetro Lió, Luciano Milanesi
Software Mentions: 11
Published: almost 10 years ago
10.3389/fgene.2021.692426
A Ferroptosis-Related Gene Signature Identified as a Novel Prognostic Biomarker for Colon Cancer
Cited by: 15
Author(s): Xin Qi, Rui Wang, Yuxin Lin, Donghui Yan, Jiachen Zuo, Jiajia Chen, Bairong Shen
Software Mentions: 11
Published: over 3 years ago
10.7554/eLife.64846
NF1 regulates mesenchymal glioblastoma plasticity and aggressiveness through the AP-1 transcription factor FOSL1
Cited by: 36
Author(s): Carolina Marques, Thomas Unterkircher, Paula Kroon, Barbara Oldrini, Annalisa Izzo, Yuliia Dramaretska, Roberto Ferrarese, Eva Kling, Oliver Schnell, Sven Nelander, Erwin F. Wagner, Latifa Bakiri, Gaetano Gargiulo, Maria Stella Carro, Massimo Squatrito
Software Mentions: 11
Published: over 3 years ago