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
10.1002/pmic.201400392
Visualization of proteomics data using R and BioconductorCited by: 46
Author(s): Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
Software Mentions: 62
Published: over 9 years ago
10.12688/f1000research.17824.2
Enhancing gene set enrichment using networksCited by: 2
Author(s): Michael Prummer
Software Mentions: 51
Published: over 5 years ago
10.1371/journal.pcbi.1007912
bigPint: A Bioconductor visualization package that makes big data pint-sizedCited by: 3
Author(s): Lindsay Rutter, Dianne Cook
Software Mentions: 47
Published: over 4 years ago
10.3389/fonc.2020.00423
Computational Oncology in the Multi-Omics Era: State of the ArtCited by: 55
Author(s): Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Software Mentions: 46
Published: over 4 years ago
10.1371/journal.pcbi.1000227
Analyzing ChIP-chip Data Using BioconductorCited by: 19
Author(s): Joern Toedling, Wolfgang Huber
Software Mentions: 39
Published: almost 16 years ago
10.12688/f1000research.22259.1
Fluent genomics with plyranges and tximetaCited by: 2
Author(s): Stuart Lee, Michael C. Lawrence, Michael I. Love
Software Mentions: 35
Published: over 4 years ago
10.12688/f1000research.9973.2
BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment testsCited by: 20
Author(s): Andrea Komljenović, Julien Roux, Julien Wollbrett, Marc Robinson‐Rechavi, Frederic Bastian
Software Mentions: 33
Published: about 6 years ago
10.3390/biology3010085
R-Based Software for the Integration of Pathway Data into Bioinformatic AlgorithmsCited by: 17
Author(s): Frank Krämer, Michaela Bayerlová, Tim Beißbarth
Software Mentions: 28
Published: over 10 years ago
10.1186/s12859-017-1905-4
ADAGE signature analysis: differential expression analysis with data-defined gene setsCited by: 15
Author(s): Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene
Software Mentions: 25
Published: almost 7 years ago
10.3389/fmolb.2020.570702
Prognostic Prediction Using a Stemness Index-Related Signature in a Cohort of Gastric CancerCited by: 27
Author(s): Xiaowei Chen, Dawei Zhang, Fei Jiang, Yan Shen, Xin Li, Xin Hu, Pingmin Wei, Xiaobing Shen
Software Mentions: 24
Published: about 4 years ago
10.1186/1751-0473-8-1
MmPalateMiRNA, an R package compendium illustrating analysis of miRNA microarray dataCited by: 11
Author(s): Guy Brock, Partha Mukhopadhyay, Vasyl Pihur, Cynthia L. Webb, Robert M. Greene, M. Michele Pisano
Software Mentions: 24
Published: almost 12 years ago
10.3389/fimmu.2021.616967
A Multi-Omics Analysis of Mucosal-Associated-Invariant T Cells Reveals Key Drivers of Distinct Modes of ActivationCited by: 12
Author(s): Kristin Schubert, Isabel Karkossa, Jana Schor, Beatrice Engelmann, Lisa Maria Steinheuer, Tony Bruns, Ulrike Rolle-Kampczyk, Jörg Hackermüller, Martin von Bergen
Software Mentions: 24
Published: over 3 years ago
10.3389/fimmu.2021.659444
Development and Validation of a CD8+ T Cell Infiltration-Related Signature for Melanoma PatientsCited by: 13
Author(s): Yuan Yuan, Zheng Zhu, Ying Lan, Saili Duan, Zijue Zhu, Xi Zhang, Guoyin Li, Hui Qü, Yao Feng, Hui Cai, Zewen Song
Software Mentions: 24
Published: over 3 years ago
10.1371/journal.pcbi.1007792
eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity researchCited by: 38
Author(s): Augusto Anguita‐Ruiz, Alberto Segura‐Delgado, Rafael Alcalá, Concepción M. Aguilera, Jesús Alcalá‐Fdez
Software Mentions: 23
Published: over 4 years ago
10.1155/2021/8020879
Novel lncRNA Panel as for Prognosis in Esophageal Squamous Cell Carcinoma Based on ceRNA Network MechanismCited by: 10
Author(s): Jin Zhang, Fei Xiao, Guangliang Qiang, Zhenrong Zhang, Qianli Ma, Hao Yang, H. Rosie Xing, Chaoyang Liang
Software Mentions: 22
Published: about 3 years ago
10.3389/fimmu.2021.632333
Immunological Feature and Transcriptional Signaling of Ly6C Monocyte Subsets From Transcriptome Analysis in Control and Hyperhomocysteinemic MiceCited by: 7
Author(s): Panpan Yang, Lu Liu, Lili Sun, Fang Pu, Nathaniel W. Snyder, Jason Saredy, Yong Ji, Wen Shen, Xuebin Qin, Qinghua Wu, Xiaofeng Yang, Hong Wang
Software Mentions: 21
Published: over 3 years ago
10.3389/fgene.2021.667936
Bioinformatic Analysis of Temporal and Spatial Proteome Alternations During InfectionsCited by: 9
Author(s): Matineh Rahmatbakhsh, Alla Gagarinova, Mohan Babu
Software Mentions: 21
Published: over 3 years ago
10.1186/s13059-016-0881-8
A survey of best practices for RNA-seq data analysisCited by: 1,691
Author(s): Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang, A Mortazavi
Software Mentions: 21
Published: almost 9 years ago
10.1186/s12864-017-4353-7
DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanismCited by: 72
Author(s): Ali Sharifi-Zarchi, Daniela Gerovska, Kenjiro Adachi, Mehdi Totonchi, Hamid Pezeshk, Ryan J. Taft, Hans R. Schöler, Hamidreza Chitsaz, Mehdi Sadeghi, Hossein Baharvand, Marcos J. Araúzo-Bravo
Software Mentions: 21
Published: almost 7 years ago
10.15252/msb.20199247
<i> <scp>STAT</scp> 3 </i> ‐dependent analysis reveals <i> <scp>PDK</scp> 4 </i> as independent predictor of recurrence in prostate cancerCited by: 34
Author(s): Monika Oberhuber, Matteo Pecoraro, Mate Rusz, Georg Oberhuber, Maritta Wieselberg, Peter Haslinger, Elisabeth Gurnhofer, Michaela Schlederer, Tanja Limberger, Sabine Lagger, Jan Pěnčík, Petra Kodajova, Sandra Högler, Georg Stockmaier, Sandra Grund-Gröschke, Fritz Aberger, Marco Bolis, Jean-Philippe Theurillat, Robert Wiebringhaus, Theresa R. Weiss, Andrea Haitel, Marc Brehme, Wolfgang Wadsak, Johannes Griss, Thomas Mohr, Alexandra Hofer, Anton Jäger, Jürgen Pollheimer, Gerda Egger, Gunda Koellensperger, Matthias Mann, Brigitte Hantusch, Lukas Kenner
Software Mentions: 21
Published: over 4 years ago
10.12688/f1000research.13577.2
Using regulatory genomics data to interpret the function of disease variants and prioritise genes from expression studiesCited by: 2
Author(s): Enrico Ferrero
Software Mentions: 21
Published: over 6 years ago
10.1016/j.xcrm.2020.100096
Treatment with Commonly Used Antiretroviral Drugs Induces a Type I/III Interferon Signature in the Gut in the Absence of HIV InfectionCited by: 11
Author(s): Sean M. Hughes, Claire Levy, Fernanda Calienes, Joanne D. Stekler, Urvashi Pandey, Lucia Vojtech, Alicia R. Berard, Kenzie Birse, Laura Noël‐Romas, Brian Richardson, Jackelyn B. Golden, Michael Cartwright, Ann C. Collier, Claire E. Stevens, Marcel E. Curlin, Timothy H. Holtz, Nelly Mugo, Elizabeth Irungu, Elly Katabira, Timothy Muwonge, Javier R. Lama, Jared M. Baeten, Adam Burgener, Jairam R. Lingappa, M. Juliana McElrath, Romel D. Mackelprang, Ian McGowan, Ross D. Cranston, Mark J. Cameron, Florian Hladik
Software Mentions: 21
Published: about 4 years ago
10.1016/j.xcrm.2020.100128
The Clinical Kinase Index: A Method to Prioritize Understudied Kinases as Drug Targets for the Treatment of CancerCited by: 32
Author(s): Derek J. Essegian, Rimpi Khurana, Vasileios Stathias, Stephan C. Schürer
Software Mentions: 21
Published: about 4 years ago
10.12688/f1000research.18456.1
A step-by-step guide to analyzing CAGE data using R/BioconductorCited by: 10
Author(s): Malte Thodberg, Albin Sandelin
Software Mentions: 20
Published: over 5 years ago
10.1186/s13059-020-02100-5
Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing dataCited by: 56
Author(s): Nikolaus Fortelny, Christoph Bock
Software Mentions: 20
Published: over 4 years ago
10.1186/1756-0500-3-277
EMA - A R package for Easy Microarray data analysisCited by: 45
Author(s): Nicolas Servant, Eléonore Gravier, Pierre Gestraud, Cécile Laurent, Caroline Paccard, Anne Biton, Isabel Martínez Brito, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupé
Software Mentions: 20
Published: almost 14 years ago
10.3390/genes11030257
mRNAsi Index: Machine Learning in Mining Lung Adenocarcinoma Stem Cell BiomarkersCited by: 61
Author(s): Yitong Zhang, Joseph T. Tseng, I-Chia Lien, Fenglan Li, Wei Wu, Hui Li
Software Mentions: 20
Published: over 4 years ago
10.15252/msb.20188746
Current best practices in single‐cell RNA‐seq analysis: a tutorialCited by: 1,173
Author(s): Malte D. Luecken, Fabian J. Theis
Software Mentions: 20
Published: over 5 years ago
10.1084/jem.20201795
Diagnostic blood RNA profiles for human acute spinal cord injuryCited by: 21
Author(s): Nikos Kyritsis, Abel Torres-Espín, Patrick G. Schupp, J. Russell Huie, Austin Chou, Xuan Duong Fernandez, Libby Thomas, Rachel Tsolinas, Debra D. Hemmerle, Lisa U. Pascual, Vineeta Singh, Jonathan Z. Pan, Jason F. Talbott, William D. Whetstone, John F. Burke, Anthony M DiGiorgio, Philip Weinstein, Geoffrey T. Manley, Sanjay S. Dhall, Adam R. Ferguson, Michael C. Oldham, Jacqueline C. Bresnahan, Michael S. Beattie
Software Mentions: 19
Published: almost 4 years ago
10.3389/fonc.2020.607727
Gene Panel of Persister Cells as a Prognostic Indicator for Tumor Repopulation After RadiationCited by: 3
Author(s): Yucui Zhao, Yanwei Song, Ruyi Zhao, Minghui Zhao, Qian Huang
Software Mentions: 18
Published: almost 4 years ago
10.3389/fonc.2021.605810
A Novel Risk Factor Model Based on Glycolysis-Associated Genes for Predicting the Prognosis of Patients With Prostate CancerCited by: 6
Author(s): Kaixuan Guo, Cong Lai, Juan Shi, Zhuang Tang, Cheng Liu, Kuiqing Li, Kailin Xu
Software Mentions: 18
Published: about 3 years ago
10.3389/fimmu.2021.620270
Non-Genomic AhR-Signaling Modulates the Immune Response in Endotoxin-Activated Macrophages After Activation by the Environmental Stressor BaPCited by: 18
Author(s): Henning Großkopf, Katharina Walter, Isabel Karkossa, Martin von Bergen, Kristin Schubert
Software Mentions: 18
Published: over 3 years ago
10.1016/j.molcel.2021.05.023
Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infectionCited by: 87
Author(s): Wael Kamel, Marko Noerenberg, Berati Cerikan, Honglin Chen, Aino I Järvelin, Mohamed Kammoun, Young Seok Lee, Shuai Ni, Manuel García-Moreno, Anna Andrejeva, Michael J. Deery, Natasha Johnson, Christopher J Neufeldt, Mirko Cortese, Michael Knight, Kathryn S. Lilley, Javier Martı̂nez, Ilan Davis, Ralf Bartenschlager, Shabaz Mohammed, Alfredo Castelló
Software Mentions: 18
Published: over 3 years ago
10.3389/fimmu.2020.01691
Leveraging Public Single-Cell and Bulk Transcriptomic Datasets to Delineate MAIT Cell Roles and Phenotypic Characteristics in Human MalignanciesCited by: 22
Author(s): Tony Yao, Parisa Shooshtari, S. M. Mansour Haeryfar
Software Mentions: 18
Published: over 4 years ago
10.1093/bioinformatics/bty947
SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics dataCited by: 19
Author(s): Jamie Soul, Timothy E. Hardingham, Raymond P. Boot-Handford, Jean-Marc Schwartz
Software Mentions: 18
Published: almost 6 years ago
10.1186/s13059-019-1805-1
Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylationCited by: 65
Author(s): Amanda J. Price, Leonardo Collado‐Torres, Н. А. Иванов, Wei Xia, Emily E. Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E. Jaffe
Software Mentions: 18
Published: about 5 years ago
10.18632/aging.103499
Multi-omics network analysis reveals distinct stages in the human aging progression in epidermal tissueCited by: 16
Author(s): Nicholas Holzscheck, Jörn Söhle, Boris Kristof, Elke Grönniger, Stefan Gallinat, Horst Wenck, Marc Winnefeld, Cassandra Falckenhayn, Lars Kaderali
Software Mentions: 18
Published: over 4 years ago
10.1186/s12859-020-03577-4
NASQAR: a web-based platform for high-throughput sequencing data analysis and visualizationCited by: 38
Author(s): Ayman Yousif, Nizar Drou, Jillian Rowe, Mohammed Khalfan, Kristin C. Gunsalus
Software Mentions: 17
Published: over 4 years ago
10.3389/fonc.2021.658165
Using Tumor-Infiltrating Immune Cells and a ceRNA Network Model to Construct a Prognostic Analysis Model of Thyroid CarcinomaCited by: 11
Author(s): Fan Zhang, Xiao‐Juan Yu, Zheyu Lin, Xichang Wang, Tengteng Gao, Di Teng, Weiping Teng
Software Mentions: 17
Published: over 3 years ago
10.1186/s12859-020-03819-5
ideal: an R/Bioconductor package for interactive differential expression analysisCited by: 18
Author(s): Fédérico Marini, Jan Linke, Harald Binder
Software Mentions: 17
Published: almost 4 years ago
10.1186/s13059-020-02104-1
Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome dataCited by: 57
Author(s): Matteo Calgaro, Chiara Romualdi, Levi Waldron, Davide Risso, Nicola Vitulo
Software Mentions: 17
Published: over 4 years ago
10.1186/s12859-021-04054-2
CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry dataCited by: 13
Author(s): Yuting Dai, Aining Xu, Jianfeng Li, Liang Wu, Shanhe Yu, Jun Chen, Wei‐Li Zhao, Xiao Jian Sun, Jinyan Huang
Software Mentions: 17
Published: over 3 years ago
10.1038/s41597-019-0171-x
A multi-omics digital research object for the genetics of sleep regulationCited by: 8
Author(s): Jan M, Nastassia Gobet, Shanaz Diessler, Paul Franken, Ioannis Xénarios
Software Mentions: 17
Published: about 5 years ago
10.1371/journal.pcbi.1006245
Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools databaseCited by: 213
Author(s): Luke Zappia, Belinda Phipson, Alicia Oshlack
Software Mentions: 17
Published: over 6 years ago
10.1038/s41597-021-00998-5
A merged microarray meta-dataset for transcriptionally profiling colorectal neoplasm formation and progressionCited by: 4
Author(s): Michael Rohr, Jordan M. Beardsley, Sai Preethi Nakkina, Xiang Zhu, Jihad Aljabban, Dexter Hadley, Deborah A. Altomare
Software Mentions: 17
Published: about 3 years ago
10.1016/j.cell.2015.01.006
Enhancer Evolution across 20 Mammalian SpeciesCited by: 626
Author(s): Diego Villar, Camille Berthelot, Sarah Aldridge, Tim Rayner, Margus Lukk, Miguel Pignatelli, Thomas J. Park, Robert Deaville, Jonathan Thor Erichsen, Anna J. Jasinska, James M. A. Turner, Mads F. Bertelsen, Elizabeth P. Murchison, Paul Flicek, Duncan T. Odom
Software Mentions: 17
Published: almost 10 years ago
10.1186/s40168-019-0725-3
Baseline microbiota composition modulates antibiotic-mediated effects on the gut microbiota and hostCited by: 43
Author(s): Aonghus Lavelle, Thomas Hoffmann, Hang-Phuong Pham, Philippe Langella, Éric Guédon, Harry Sokol
Software Mentions: 16
Published: over 5 years ago
10.3389/fonc.2021.690129
A Tumor Progression Related 7-Gene Signature Indicates Prognosis and Tumor Immune Characteristics of Gastric CancerCited by: 6
Author(s): Fen Liu, Zongcheng Yang, Lixin Zheng, Wei Shao, Xiujie Cui, Yue Wang, Jihui Jia, Yue Fu
Software Mentions: 16
Published: over 3 years ago
10.1186/s13059-014-0550-8
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2Cited by: 49,504
Author(s): Michael I. Love, Wolfgang Huber, Simon Anders
Software Mentions: 16
Published: almost 10 years ago
10.3390/cancers12040957
Pan-Cancer Analysis of Radiotherapy Benefits and Immune Infiltration in Multiple Human CancersCited by: 10
Author(s): Pengbo Wen, Yang Gao, Bin Chen, Xiaojing Qi, Guanshuo Hu, An Xu, Junfeng Xia, Lijun Wu, Lu Han, Guoping Zhao
Software Mentions: 16
Published: over 4 years ago
10.1186/1471-2105-11-237
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip dataCited by: 868
Author(s): Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson, Hervé Pagès, Simon Lin, David S. Lapointe, Michael R. Green
Software Mentions: 16
Published: over 14 years ago
10.1186/1471-2105-9-439
CMA – a comprehensive Bioconductor package for supervised classification with high dimensional dataCited by: 90
Author(s): Martin Slawski, Martin Däumer, Anne‐Laure Boulesteix
Software Mentions: 16
Published: about 16 years ago
10.1038/s41598-020-69683-8
Concomitant DNA methylation and transcriptome signatures define epidermal responses to acute solar UV radiationCited by: 5
Author(s): Nicholas Holzscheck, Jörn Söhle, T. Schläger, Cassandra Falckenhayn, Elke Grönniger, Ludger Kolbe, Horst Wenck, Lara Terstegen, Lars Kaderali, Marc Winnefeld, Katharina Gorges
Software Mentions: 16
Published: over 4 years ago
10.1186/s13059-021-02388-x
Gene set enrichment analysis for genome-wide DNA methylation dataCited by: 61
Author(s): Jovana Maksimovic, Alicia Oshlack, Belinda Phipson
Software Mentions: 16
Published: over 3 years ago
10.3389/fonc.2021.644416
An Inflammatory Response-Related Gene Signature Can Impact the Immune Status and Predict the Prognosis of Hepatocellular CarcinomaCited by: 62
Author(s): Zhuo Lin, Xu Qian, Dan Miao, Fang Yu
Software Mentions: 16
Published: over 3 years ago
10.1186/s12935-020-01571-7
RETRACTED ARTICLE: Aging-related tumor associated fibroblasts changes could worsen the prognosis of GBM patientsCited by: 7
Author(s): Hongwang Song, Xiaojun Fu, Chenxing Wu, Shouwei Li
Software Mentions: 16
Published: about 4 years ago
10.12688/f1000research.16198.2
scClustViz – Single-cell RNAseq cluster assessment and visualizationCited by: 25
Author(s): Brendan T. Innes, Gary D. Bader
Software Mentions: 16
Published: over 5 years ago
10.12688/f1000research.15398.3
Swimming downstream: statistical analysis of differential transcript usage following Salmon quantificationCited by: 53
Author(s): Michael I. Love, Charlotte Soneson, Rob Patro
Software Mentions: 16
Published: about 6 years ago
10.3390/biom10121606
A Customizable Analysis Flow in Integrative Multi-OmicsCited by: 14
Author(s): Samuel M. Lancaster, Akshay Sanghi, Si Wu, M Snyder
Software Mentions: 15
Published: almost 4 years ago
10.3389/fcell.2021.642724
Identification of Stemness-Related Genes for Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma by Integrated Bioinformatics AnalysisCited by: 5
Author(s): Hongjun Guo, Siqiao Wang, Min Kyung Ju, Penghui Yan, Weiwei Sun, Zhenyu Li, Siyu Wu, Ruoyi Lin, Shuyuan Xian, Daoke Yang, Jun Wang, Zongqiang Huang
Software Mentions: 15
Published: over 3 years ago
10.1371/journal.pone.0183417
Association of gene expression with biomass content and composition in sugarcaneCited by: 23
Author(s): Nam V. Hoang, Agnelo Furtado, Angela O'Keeffe, Frederik C. Botha, Robert J. Henry
Software Mentions: 15
Published: about 7 years ago
10.3389/fmicb.2015.00104
Long-term forest soil warming alters microbial communities in temperate forest soilsCited by: 237
Author(s): Kristen M. DeAngelis, Grace Pold, Begüm D. Topçuoğlu, Linda T. A. van Diepen, Rebecca Varney, Jeffrey L. Blanchard, Jerry M. Melillo, Serita D. Frey
Software Mentions: 15
Published: over 9 years ago
10.12688/f1000research.8987.2
From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipelineCited by: 415
Author(s): Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth
Software Mentions: 15
Published: over 8 years ago
10.1186/s12859-015-0719-5
mAPKL: R/ Bioconductor package for detecting gene exemplars and revealing their characteristicsCited by: 3
Author(s): Αλέξανδρος Σακελλαρίου, George M. Spyrou
Software Mentions: 15
Published: about 9 years ago
10.3389/fonc.2021.650153
Identification and Validation of a Prognostic Immune-Related Alternative Splicing Events Signature for GliomaCited by: 5
Author(s): Minjie Wang, Zhongqiang Zhou, Jianglin Zheng, Wenjun Xiao, Jun Zhu, Chaocai Zhang, Xueshi Jiang
Software Mentions: 15
Published: over 3 years ago
10.1186/s12864-020-06856-9
mitch: multi-contrast pathway enrichment for multi-omics and single-cell profiling dataCited by: 28
Author(s): Antony Kaspi, Mark Ziemann
Software Mentions: 15
Published: over 4 years ago
10.1038/s41598-021-88209-4
Identification of transcriptional subtypes in lung adenocarcinoma and squamous cell carcinoma through integrative analysis of microarray and RNA sequencing dataCited by: 6
Author(s): François Fauteux, Anuradha Surendra, Scott McComb, Youlian Pan, Jonathan D. Hill
Software Mentions: 15
Published: over 3 years ago
10.3390/cells8111321
Transcriptional Regulation of Autophagy Genes via Stage-Specific Activation of CEBPB and PPARG during Adipogenesis: A Systematic Study Using Public Gene Expression and Transcription Factor Binding DatasetsCited by: 16
Author(s): Mahmoud Ahmed, Trang Huyen Lai, Jin Seok Hwang, Sahib Zada, Trang Minh Pham, Deok Ryong Kim
Software Mentions: 15
Published: about 5 years ago
10.1186/s13059-020-02132-x
A systematic evaluation of single-cell RNA-sequencing imputation methodsCited by: 156
Author(s): Wenpin Hou, Zhicheng Ji, Hongkai Ji, Stephanie Hicks
Software Mentions: 15
Published: about 4 years ago
10.3389/fcell.2021.671736
Identification of a Novel Immune Landscape Signature for Predicting Prognosis and Response of Endometrial Carcinoma to Immunotherapy and ChemotherapyCited by: 6
Author(s): Jinhui Liu, Yichun Wang, Jie Mei, Song Nie, Yan Zhang
Software Mentions: 15
Published: over 3 years ago
10.3390/life11070716
Single-Cell Transcriptome Profiling Simulation Reveals the Impact of Sequencing Parameters and Algorithms on ClusteringCited by: 0
Author(s): Yunhe Liu, Aoshen Wu, Xueqing Peng, Xiaona Liu, Gang Liu, Lei Liu
Software Mentions: 15
Published: over 3 years ago
10.26508/lsa.202000766
Egr2 and 3 control inflammation, but maintain homeostasis, of PD-1<sup>high</sup> memory phenotype CD4 T cellsCited by: 6
Author(s): Alistair L. J. Symonds, Wei Zheng, Tizong Miao, Ang Li, Tieshang Wang, Ruth Kiome, Xiaofeng Hou, Suling Li, Ping Wang
Software Mentions: 15
Published: over 4 years ago
10.1186/s12967-021-02773-x
Multi-omics characterization and validation of invasiveness-related molecular features across multiple cancer typesCited by: 5
Author(s): Guoshu Bi, Jiaqi Liang, Yuansheng Zheng, Runmei Li, Mengnan Zhao, Yiwei Huang, Cheng Zhan, Songtao Xu, Hong Fan
Software Mentions: 15
Published: over 3 years ago
10.1186/s12916-020-01686-8
In utero and childhood exposure to tobacco smoke and multi-layer molecular signatures in childrenCited by: 19
Author(s): Marta Vives-Usano, Carles Hernández-Ferrer, Léa Maitre, Carlos Ruiz‐Arenas, Sandra Andrušaitytė, Eva Borràs, Ángel Carracedo, Maribel Casas, Leda Chatzi, Muireann Coen, Xavier Estivill, Juan R. González, Kristine B. Gützkow, Hector C. Keun, Chung-Ho E Lau, Solène Cadiou, Johanna Lepeule, Dan Mason, Inés Quintela, Oliver Robinson, Eduard Sabidó, Gillian Santorelli, Per E. Schwarze, Alexandros P. Siskos, Rémy Slama, Marina Vafeiadi, Eulàlia Martı́, Martine Vrijheid, Mariona Bustamante
Software Mentions: 14
Published: about 4 years ago
10.1186/s12859-016-0884-1
Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysisCited by: 62
Author(s): Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer
Software Mentions: 14
Published: almost 9 years ago
10.1186/s12967-021-02894-3
Identification of immune subtypes of cervical squamous cell carcinoma predicting prognosis and immunotherapy responsesCited by: 8
Author(s): Yimin Li, Shun Lü, Shubin Wang, Xinhao Peng, Jinyi Lang
Software Mentions: 14
Published: over 3 years ago
10.1038/s42003-019-0554-8
Single-cell landscape in mammary epithelium reveals bipotent-like cells associated with breast cancer risk and outcomeCited by: 37
Author(s): Weiyan Chen, Samuel Morabito, Kai Kessenbrock, Tariq Enver, Kerstin B. Meyer, Andrew E. Teschendorff
Software Mentions: 14
Published: about 5 years ago
10.1186/s12859-015-0683-0
diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C dataCited by: 172
Author(s): Aaron T. L. Lun, Gordon K. Smyth
Software Mentions: 14
Published: about 9 years ago
10.1371/journal.pcbi.1009317
Meta-analysis of transcriptomic data reveals clusters of consistently deregulated gene and disease ontologies in Down syndromeCited by: 11
Author(s): Ilario De Toma, Cesar Sierra, Mara Dierssen
Software Mentions: 14
Published: about 3 years ago
10.7717/peerj.11880
Integrated bioinformatics analysis of the NEDD4 family reveals a prognostic value of <i>NEDD4L</i> in clear-cell renal cell cancerCited by: 6
Author(s): Hui Zhao, Junjun Zhang, Xiaoliang Fu, Dongdong Mao, Xuesen Qi, Shuai Liang, Gang Ma, Zewen Song, Ru Yang, Zhenni Guo, Binghua Tong, Meiqing Sun, Baile Zuo, Guoyin Li
Software Mentions: 14
Published: about 3 years ago
10.1186/s12859-021-04193-6
Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencingCited by: 32
Author(s): Zachary D Wallen
Software Mentions: 14
Published: over 3 years ago
10.1186/s12967-021-02952-w
Molecular subtype identification and prognosis stratification by a metabolism-related gene expression signature in colorectal cancerCited 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
10.1007/s00401-021-02343-x
Cross-platform transcriptional profiling identifies common and distinct molecular pathologies in Lewy body diseasesCited by: 23
Author(s): Rahel Feleke, Regina H. Reynolds, Amy M. Smith, Bension S. Tilley, Sarah A. Gagliano Taliun, John Hardy, Paul M. Matthews, Steve Gentleman, David R. Owen, Michael R. Johnson, Prashant K. Srivastava, Mina Ryten
Software Mentions: 14
Published: over 3 years ago
10.1186/s12859-016-0971-3
GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression dataCited by: 20
Author(s): Kévin Rue-Albrecht, Paul A. McGettigan, Belinda Hernández, Nicolas C. Nalpas, David A. Magee, Andrew Parnell, Stephen V. Gordon, David E. MacHugh
Software Mentions: 14
Published: over 8 years ago
10.3389/fimmu.2020.606164
Six Immune Associated Genes Construct Prognostic Model Evaluate Low-Grade GliomaCited by: 32
Author(s): Yin Qiu Tan, Yun Tao Li, Teng Feng Yan, Yang Xu, Bao Hui Liu, Ji An Yang, Yang Xue, Qianxue Chen, Hong Bo Zhang
Software Mentions: 14
Published: almost 4 years ago
10.3389/fimmu.2021.557994
Investigation of Genetic Determinants of Glioma Immune Phenotype by Integrative Immunogenomic Scale AnalysisCited by: 10
Author(s): Binghao Zhao, Yuekun Wang, Yaning Wang, Congxin Dai
Software Mentions: 14
Published: over 3 years ago
10.1038/s41598-020-80165-9
Multi-level remodelling of chromatin underlying activation of human T cellsCited by: 23
Author(s): Naiara G. Bediaga, Hannah D. Coughlan, Timothy M. Johanson, Alexandra L. Garnham, Gaetano Naselli, Jan Schröder, Liam G. Fearnley, Esther Bandala‐Sanchez, Rhys S. Allan, Gordon K. Smyth, Leonard C. Harrison
Software Mentions: 14
Published: almost 4 years ago
10.1186/s13059-018-1484-3
CTCF maintains regulatory homeostasis of cancer pathwaysCited by: 39
Author(s): Sarah J. Aitken, Ximena Ibarra-Soria, Elissavet Kentepozidou, Paul Flicek, Christine Feig, John C. Marioni, Duncan T. Odom
Software Mentions: 14
Published: about 6 years ago
10.1093/bioinformatics/btw777
Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in RCited by: 1,059
Author(s): Davis J. McCarthy, Kieran R Campbell, Aaron T. L. Lun, Quin F. Wills
Software Mentions: 14
Published: almost 8 years ago
10.18632/aging.203353
Development and validation of an intra-tumor heterogeneity-related signature to predict prognosis of bladder cancer: a study based on single-cell RNA-seqCited by: 7
Author(s): Ranran Zhou, Jingjing Liang, Qi Chen, Haijun Tian, Cheng Yang, Cundong Liu
Software Mentions: 14
Published: over 3 years ago
10.3389/fcell.2021.657667
Identification of the Prognostic Significance of Somatic Mutation-Derived LncRNA Signatures of Genomic Instability in Lung AdenocarcinomaCited by: 31
Author(s): Geng Wang, Zhi Lv, Jinshuo Fan, Jing Xu, Kaimin Mao, Zhengrong Yin, Wanlu Qing, Yang Jin
Software Mentions: 14
Published: over 3 years ago
10.3389/fimmu.2021.646523
Systematic Pan-Cancer Analysis Identifies TREM2 as an Immunological and Prognostic BiomarkerCited by: 57
Author(s): Xin Cheng, Xiaowei Wang, Kechao Nie, Lin Cheng, Zheyu Zhang, Yang Hu, Weijun Peng
Software Mentions: 14
Published: over 3 years ago
10.1186/s12859-018-2486-6
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq dataCited by: 650
Author(s): Xijin Ge, Eun Wo Son, Runan Yao
Software Mentions: 14
Published: almost 6 years ago
10.3389/fcell.2020.592490
Transcriptome Sequencing Reveals Potential Roles of ICOS in Primary Sjögren’s SyndromeCited by: 19
Author(s): Jing Luo, Xin Liao, Lihe Zhang, Xin Xu, Senhong Ying, Mengjiao Yu, Lixia Zhu, Suxian Lin, Xiaobing Wang
Software Mentions: 14
Published: almost 4 years ago
10.1038/s41598-021-97362-9
N6-methylandenosine-related lncRNAs play an important role in the prognosis and immune microenvironment of pancreatic ductal adenocarcinomaCited by: 5
Author(s): Yuhai Hu, Yiping Chen
Software Mentions: 14
Published: about 3 years ago
10.3389/fgene.2021.702072
Characterization of Modification Patterns, Biological Function, Clinical Implication, and Immune Microenvironment Association of m6A Regulators in Pancreatic CancerCited by: 5
Author(s): Kun Fang, Hairong Qu, Jiapei Wang, Desheng Tang, Changsheng Yan, Jiamin Ma, Lei Gao
Software Mentions: 14
Published: about 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 gliomaCited 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: about 4 years ago
10.3389/fonc.2020.573295
Differential Expression Analysis Revealing CLCA1 to Be a Prognostic and Diagnostic Biomarker for Colorectal CancerCited by: 11
Author(s): Fang-Ze Wei, Shiwen Mei, Zhijie Wang, Jianan Chen, Huan Shen, Fen Zhao, Juan Li, Zheng Liu, Qian Liu
Software Mentions: 14
Published: about 4 years ago
10.3389/fgene.2020.522125
Identification of Prognostic Markers in Cholangiocarcinoma Using Altered DNA Methylation and Gene Expression ProfilesCited by: 11
Author(s): Nitish K. Mishra, Meng Niu, Siddesh Southekal, Prachi Bajpai, Amr Elkholy, Upender Manne, Chittibabu Guda
Software Mentions: 14
Published: about 4 years ago
10.3389/fgene.2021.689406
Reference Transcriptomes of Porcine Peripheral Immune Cells Created Through Bulk and Single-Cell RNA SequencingCited by: 26
Author(s): Júber Herrera-Uribe, Jayne E Wiarda, Sathesh K Sivasankaran, Lance Daharsh, Haibo Li, Kristen A Byrne, Timothy P. L. Smith, Joan K. Lunney, Crystal L. Loving, Christopher K. Tuggle
Software Mentions: 14
Published: over 3 years ago