bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.1002/pmic.201400392

Visualization of proteomics data using R and Bioconductor
Cited 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 networks
Cited 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-sized
Cited 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 Art
Cited by: 55
Author(s): Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Software Mentions: 46
Published: over 4 years ago

10.12688/f1000research.22259.1

Fluent genomics with plyranges and tximeta
Cited by: 2
Author(s): Stuart Lee, Michael C. Lawrence, Michael I. Love
Software Mentions: 35
Published: almost 5 years ago

Predictive features of gene expression variation reveal mechanistic link with differential expression
Cited by: 36
Author(s): Olga M. Sigalova, Amirreza Shaeiri, Mattia Forneris, Eileen E. M. Furlong, Judith B. Zaugg
Software Mentions: 30
Published: over 4 years ago

10.1186/s13073-021-00910-1

Landscape and selection of vaccine epitopes in SARS-CoV-2
Cited by: 21
Author(s): Christof C. Smith, Kelly Olsen, Kaylee M. Gentry, Maria J. Sambade, Wolfgang Beck, Jason Garness, Sarah Entwistle, Caryn Willis, Steven Vensko, Allison Woods, Misha Fini, Brandon Carpenter, Eric D. Routh, Julia Kodysh, Timothy J. O’Donnell, Carsten Haber, Kirsten Heiß, Volker Stadler, Erik Garrison, Adam Sandor, Jenny P.-Y. Ting, Jared Weiss, Krzysztof Krajewski, Oliver C. Grant, Robert J. Woods, Mark T. Heise, Benjamin G. Vincent, Alex Rubinsteyn
Software Mentions: 27
Published: over 3 years ago

10.1084/jem.20210915

Blood transcriptomics reveal the evolution and resolution of the immune response in tuberculosis
Cited by: 27
Author(s): Olivier Tabone, Raman Verma, Akul Singhania, Probir Chakravarty, William J. Branchett, Christine M. Graham, Jo Lee, Trần Thị Huyền Trang, Frédéric Reynier, Philippe Leissner, Karine Kaiser, Marc Rodrigue, Gerrit Woltmann, Pranabashis Haldar, Anne O’Garra
Software Mentions: 27
Published: over 3 years ago

10.3389/fimmu.2021.616967

A Multi-Omics Analysis of Mucosal-Associated-Invariant T Cells Reveals Key Drivers of Distinct Modes of Activation
Cited 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

10.1016/j.cell.2019.07.038

A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana
Cited by: 237
Author(s): Anna-Lena Van de Weyer, Freddy Monteiro, Oliver J. Furzer, Marc T. Nishimura, Volkan Çevik, Kamil Witek, Jonathan D. G. Jones, Jeffery L. Dangl, Detlef Weigel, Felix Bemm
Software Mentions: 23
Published: over 5 years ago

10.1186/s13072-016-0095-z

EpiMINE, a computational program for mining epigenomic data
Cited by: 11
Author(s): Sri Ganesh Jammula, Diego Pasini
Software Mentions: 23
Published: about 8 years ago

10.1038/s41598-020-78469-x

Cerina: systematic circRNA functional annotation based on integrative analysis of ceRNA interactions
Cited by: 14
Author(s): Jacob Cardenas, Uthra Balaji, Jin Gu
Software Mentions: 23
Published: about 4 years ago

10.1016/j.patter.2021.100322

The role of metadata in reproducible computational research
Cited by: 38
Author(s): Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Karthik Ram, Jane Greenberg
Software Mentions: 21
Published: over 3 years ago

10.15252/msb.20199247

<scp>STAT</scp> 3 ‐dependent analysis reveals <scp>PDK</scp> 4 as independent predictor of recurrence in prostate cancer
Cited 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

10.1186/s13059-020-02136-7

pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools
Cited by: 53
Author(s): Pierre-Luc Germain, Anthony Sonrel, Mark D. Robinson
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 studies
Cited by: 2
Author(s): Enrico Ferrero
Software Mentions: 21
Published: almost 7 years ago

10.1186/s13059-016-0881-8

A survey of best practices for RNA-seq data analysis
Cited 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/s13059-020-1929-3

From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis
Cited by: 231
Author(s): Feng Yan, David Powell, David Curtis, Nicholas C. Wong
Software Mentions: 21
Published: almost 5 years ago

10.12688/f1000research.18456.1

A step-by-step guide to analyzing CAGE data using R/Bioconductor
Cited by: 10
Author(s): Malte Thodberg, Albin Sandelin
Software Mentions: 20
Published: over 5 years ago

10.3390/cancers13092163

Spatial Distribution of Private Gene Mutations in Clear Cell Renal Cell Carcinoma
Cited by: 10
Author(s): Ariane L. Moore, Aashil A. Batavia, Jack Kuipers, Jochen Singer, Elodie Burcklen, Peter Schraml, Christian Beisel, Holger Moch, Niko Beerenwinkel
Software Mentions: 20
Published: over 3 years ago

10.7554/eLife.51254

Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments
Cited by: 102
Author(s): Christopher Jackson, Dayanne M. Castro, Giuseppe-Antonio Saldi, Richard Bonneau, David Gresham
Software Mentions: 20
Published: almost 5 years ago

10.15252/msb.20188746

Current best practices in single‐cell RNA‐seq analysis: a tutorial
Cited by: 1,173
Author(s): Malte D. Luecken, Fabian J. Theis
Software Mentions: 20
Published: over 5 years ago

10.1371/journal.pcbi.1007664

Tximeta: Reference sequence checksums for provenance identification in RNA-seq
Cited by: 122
Author(s): Michael I. Love, Charlotte Soneson, Peter Hickey, Lisa K. Johnson, Nicholas Pierce, Lori Shepherd, Martin Morgan, Rob Patro
Software Mentions: 19
Published: almost 5 years ago

10.1186/s12859-016-1241-0

systemPipeR: NGS workflow and report generation environment
Cited by: 148
Author(s): Tyler W. H. Backman, Thomas Girke
Software Mentions: 19
Published: over 8 years ago

10.3390/cancers12040948

Reconstruction of Ewing Sarcoma Developmental Context from Mass-Scale Transcriptomics Reveals Characteristics of EWSR1-FLI1 Permissibility
Cited by: 23
Author(s): Henry E. Miller, Aparna Gorthi, Nicklas Bassani, Liesl A. Lawrence, Brian S. Iskra, Alexander J.R. Bishop
Software Mentions: 19
Published: over 4 years ago

10.1016/j.cell.2020.12.016

Spatiotemporal analysis of human intestinal development at single-cell resolution
Cited by: 215
Author(s): David Fawkner-Corbett, Agne Antanaviciute, Kaushal Parikh, Marta Jagielowicz, Ana Sousa Gerós, Tarun Gupta, Neil Ashley, Doran Khamis, Darren J. Fowler, Edward Morrissey, Christine M. Cunningham, Johnson Prv., Hashem Koohy, Alison Simmons
Software Mentions: 18
Published: almost 4 years ago

10.20517/jtgg.2020.51

Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seq
Cited by: 2
Author(s): Brandon Lieberman, Meena Kusi, Chia-Nung Hung, Chih-Wei Chou, Ning He, Yen‐Yi Ho, Josephine A. Taverna, Tim Hui-Ming Huang, Chun-Liang Chen
Software Mentions: 18
Published: almost 5 years ago

10.1371/journal.pone.0194899

Investigation of the seasonal microbiome of Anopheles coluzzii mosquitoes in Mali
Cited by: 34
Author(s): Benjamin J Krajacich, Diana L. Huestis, Adama Dao, Alpha Seydou Yaro, Moussa Diallo, Asha Krishna, Jianchu Xu, Tovi Lehmann
Software Mentions: 18
Published: over 6 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 infection
Cited 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

10.1002/1878-0261.12960

KRAS mutant rectal cancer cells interact with surrounding fibroblasts to deplete the extracellular matrix
Cited by: 6
Author(s): Jin K. Kim, Michael R. Marco, Seo‐Hyun Choi, Xuan Qu, Chin-Tung Chen, Moshe Elkabets, Lauren Fairchild, Oliver Chow, Francisco M. Barriga, Lukas E. Dow, Kevin P. O’Rourke, Bryan Szeglin, Dmitry Yarilin, Sho Fujisawa, Katia Manova‐Todorova, Philip B. Paty, Jinru Shia, Christina Leslie, J. Joshua Smith, Scott W. Lowe, Raphael Pelossof, Francisco Sánchez-Vega, Julio García-Aguilar
Software Mentions: 18
Published: over 3 years ago

10.1186/s12859-019-2879-1

pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components
Cited by: 146
Author(s): Fédérico Marini, Harald Binder
Software Mentions: 18
Published: over 5 years ago

10.18632/aging.103499

Multi-omics network analysis reveals distinct stages in the human aging progression in epidermal tissue
Cited 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

10.1128/mBio.01054-19

Microbial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial Signatures
Cited by: 28
Author(s): Miles Richardson, Neil Gottel, Jack A. Gilbert, Simon Lax
Software Mentions: 18
Published: over 5 years ago

10.1186/s40168-021-01100-2

Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantation
Cited by: 31
Author(s): Anna Cäcilia Ingham, Katrine Kielsen, Hanne Mordhorst, Marianne Ifversen, Frank Møller Aarestrup, Klaus Müller, Sünje Johanna Pamp
Software Mentions: 18
Published: over 3 years ago

10.1093/bioinformatics/bty947

SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data
Cited by: 19
Author(s): Jamie Soul, Timothy E. Hardingham, Raymond P. Boot-Handford, Jean-Marc Schwartz
Software Mentions: 18
Published: about 6 years ago

10.1186/s12859-020-03577-4

NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization
Cited by: 38
Author(s): Ayman Yousif, Nizar Drou, Jillian Rowe, Mohammed Khalfan, Kristin C. Gunsalus
Software Mentions: 17
Published: over 4 years ago

10.1371/journal.pcbi.1003531

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
Cited by: 2,083
Author(s): Paul J. McMurdie, Susan Holmes
Software Mentions: 17
Published: over 10 years ago

10.1371/journal.pcbi.1006245

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database
Cited by: 213
Author(s): Luke Zappia, Belinda Phipson, Alicia Oshlack
Software Mentions: 17
Published: over 6 years ago

10.1186/s12859-020-03819-5

ideal: an R/Bioconductor package for interactive differential expression analysis
Cited by: 18
Author(s): Fédérico Marini, Jan Linke, Harald Binder
Software Mentions: 17
Published: about 4 years ago

10.1016/j.cell.2019.12.013

Identification of a Master Regulator of Differentiation in Toxoplasma
Cited by: 154
Author(s): Benjamin S. Waldman, Dominic Schwarz, Marc H. Wadsworth, Jeroen P. J. Saeij, Alex K. Shalek, Sebastian Lourido
Software Mentions: 17
Published: almost 5 years ago

10.3389/fgene.2019.00499

ABioTrans: A Biostatistical Tool for Transcriptomics Analysis
Cited by: 6
Author(s): Zou Yutong, Thuy Tien Bui, Kumar Selvarajoo
Software Mentions: 17
Published: over 5 years ago

10.1186/s13059-020-02104-1

Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data
Cited by: 57
Author(s): Matteo Calgaro, Chiara Romualdi, Levi Waldron, Davide Risso, Nicola Vitulo
Software Mentions: 17
Published: over 4 years ago

10.1016/j.xpro.2021.100768

A computational approach for identification of core modules from a co-expression network and GWAS data
Cited by: 0
Author(s): Olivia L. Sabik, Cheryl Ackert‐Bicknell, Charles R. Farber
Software Mentions: 16
Published: over 3 years ago

10.12688/f1000research.16198.2

scClustViz – Single-cell RNAseq cluster assessment and visualization
Cited by: 25
Author(s): Brendan T. Innes, Gary D. Bader
Software Mentions: 16
Published: almost 6 years ago

10.12688/f1000research.15398.3

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification
Cited by: 53
Author(s): Michael I. Love, Charlotte Soneson, Rob Patro
Software Mentions: 16
Published: about 6 years ago

10.1186/s13059-014-0550-8

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Cited by: 49,504
Author(s): Michael I. Love, Wolfgang Huber, Simon Anders
Software Mentions: 16
Published: about 10 years ago

10.12688/f1000research.27268.1

rANOMALY: AmplicoN wOrkflow for Microbial community AnaLYsis
Cited by: 16
Author(s): Sébastien Theil, Étienne Rifa
Software Mentions: 16
Published: almost 4 years ago

10.7150/ijms.53531

Identification novel prognostic signatures for Head and Neck Squamous Cell Carcinoma based on ceRNA network construction and immune infiltration analysis
Cited by: 18
Author(s): Haiting Zhou, Yi He, Lingling Li, Cheng Wu, Guoqing Hu
Software Mentions: 16
Published: almost 4 years ago

10.7554/eLife.21883

Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex
Cited by: 72
Author(s): Lucas T. Gray, Zizhen Yao, Thuc Nghi Nguyen, Tae Kyung Kim, Hongkui Zeng, Bosiljka Tasic
Software Mentions: 16
Published: almost 8 years ago

10.1186/s40168-019-0725-3

Baseline microbiota composition modulates antibiotic-mediated effects on the gut microbiota and host
Cited 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

10.1371/journal.pone.0195112

Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats
Cited by: 43
Author(s): Edna Chiang, Marian L. Schmidt, Michelle A. Berry, Bopaiah A. Biddanda, Ashley M. Burtner, Thomas H. Johengen, Danna Palladino, Vincent J. Denef
Software Mentions: 16
Published: over 6 years ago

10.3390/ijms22062822

A Detailed Catalogue of Multi-Omics Methodologies for Identification of Putative Biomarkers and Causal Molecular Networks in Translational Cancer Research
Cited by: 6
Author(s): Efstathios Iason Vlachavas, Jonas Bohn, Frank Ückert, Sylvia Nürnberg
Software Mentions: 16
Published: almost 4 years ago

10.1038/s41598-020-69683-8

Concomitant DNA methylation and transcriptome signatures define epidermal responses to acute solar UV radiation
Cited 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

10.3390/ijms21239157

NF-Y Overexpression in Liver Hepatocellular Carcinoma (HCC)
Cited by: 16
Author(s): Eugenia Bezzecchi, Mirko Ronzio, Roberto Mantovani, Diletta Dolfini
Software Mentions: 15
Published: about 4 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 Datasets
Cited 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

10.1093/gigascience/giy123

PiGx: reproducible genomics analysis pipelines with GNU Guix
Cited by: 51
Author(s): Ricardo Wurmus, Bora Uyar, Brendan Osberg, Vedran Franke, Alexander Gosdschan, Katarzyna Wreczycka, Jonathan Ronen, Altuna Akalin
Software Mentions: 15
Published: about 6 years ago

10.3390/cancers13123089

A Comprehensive Bioinformatics Analysis of Notch Pathways in Bladder Cancer
Cited by: 12
Author(s): Chuan Zhang, Mandy Berndt‐Paetz, Jochen Neuhaus
Software Mentions: 15
Published: over 3 years ago

10.3390/biom10121606

A Customizable Analysis Flow in Integrative Multi-Omics
Cited by: 14
Author(s): Samuel M. Lancaster, Akshay Sanghi, Si Wu, M Snyder
Software Mentions: 15
Published: about 4 years ago

10.1371/journal.pone.0183417

Association of gene expression with biomass content and composition in sugarcane
Cited by: 23
Author(s): Nam V. Hoang, Agnelo Furtado, Angela O'Keeffe, Frederik C. Botha, Robert J. Henry
Software Mentions: 15
Published: over 7 years ago

10.1136/jitc-2020-000705

SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery
Cited by: 17
Author(s): Siwen Hu‐Lieskovan, Srabani Bhaumik, Kavita M. Dhodapkar, Jean‐Charles Grivel, Sumati Gupta, Brent A. Hanks, Sylvia Janetzki, Thomas O. Kleen, Yoshinobu Koguchi, Amanda W. Lund, Cristina Maccalli, Yolanda D. Mahnke, Ruslan D. Novosiadly, Senthamil R. Selvan, Tasha N. Sims, Yingdong Zhao, Holden T. Maecker
Software Mentions: 15
Published: about 4 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 pipeline
Cited by: 415
Author(s): Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth
Software Mentions: 15
Published: over 8 years ago

10.3389/fimmu.2020.00082

Fc Receptor-Like 6 (FCRL6) Discloses Progenitor B Cell Heterogeneity That Correlates With Pre-BCR Dependent and Independent Pathways of Natural Antibody Selection
Cited by: 7
Author(s): Kazuhito Honjo, Woong-Jai Won, R. Glenn King, Lara Ianov, David K. Crossman, Juliet Easlick, Mikhail A. Shakhmatov, Mohamed Khass, André M. Vale, Robert P. Stephan, Ran Li, Randall S. Davis
Software Mentions: 15
Published: almost 5 years ago

10.1186/s13059-020-02116-x

Integrative analyses of single-cell transcriptome and regulome using MAESTRO
Cited by: 107
Author(s): Chenfei Wang, Dongqing Sun, Xin Huang, Changxin Wan, Ziyi Li, Ya Han, Qian Qin, Jingyu Fan, Xintao Qiu, Yingtian Xie, Clifford A. Meyer, Myles Brown, Ming Tang, Henry W. Long, Tao Liu, X. Shirley Liu
Software Mentions: 15
Published: over 4 years ago

10.26508/lsa.202000766

Egr2 and 3 control inflammation, but maintain homeostasis, of PD-1high memory phenotype CD4 T cells
Cited 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/s12864-020-06856-9

mitch: multi-contrast pathway enrichment for multi-omics and single-cell profiling data
Cited by: 28
Author(s): Antony Kaspi, Mark Ziemann
Software Mentions: 15
Published: over 4 years ago

10.1186/s12859-017-1994-0

PIVOT: platform for interactive analysis and visualization of transcriptomics data
Cited by: 30
Author(s): Qin Zhu, Stephen Fisher, Hannah Dueck, Sarah A. Middleton, Mugdha Khaladkar, Junhyong Kim
Software Mentions: 15
Published: almost 7 years ago

10.1371/journal.pone.0256196

Finding differentially expressed sRNA-Seq regions with srnadiff
Cited by: 2
Author(s): Matthias Zytnicki, Ignacio González
Software Mentions: 15
Published: over 3 years ago

10.3390/genes12071044

CircIMPACT: An R Package to Explore Circular RNA Impact on Gene Expression and Pathways
Cited by: 3
Author(s): Alessia Buratin, Enrico Gaffo, Anna Dal Molin, Stefania Bortoluzzi
Software Mentions: 15
Published: over 3 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 data
Cited by: 6
Author(s): François Fauteux, Anuradha Surendra, Scott McComb, Youlian Pan, Jonathan D. Hill
Software Mentions: 15
Published: over 3 years ago

10.1155/2020/8833972

An Epithelial-Mesenchymal Transition (EMT) Preoperative Nomogram for Prediction of Lymph Node Metastasis in Bladder Cancer (BLCA)
Cited by: 5
Author(s): Rui Cao, Bo Ma, Gang Wang, Yaoyi Xiong, Ye Tian, Lushun Yuan
Software Mentions: 14
Published: about 4 years ago

10.1007/s00401-021-02343-x

Cross-platform transcriptional profiling identifies common and distinct molecular pathologies in Lewy body diseases
Cited 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

10.1371/journal.pcbi.1009317

Meta-analysis of transcriptomic data reveals clusters of consistently deregulated gene and disease ontologies in Down syndrome
Cited by: 11
Author(s): Ilario De Toma, Cesar Sierra, Mara Dierssen
Software Mentions: 14
Published: about 3 years ago

10.1186/s12859-016-0884-1

Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis
Cited by: 62
Author(s): Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer
Software Mentions: 14
Published: almost 9 years ago

10.1371/journal.pone.0248185

Gut microbiota profiles in diarrheic patients with co-occurrence of Clostridioides difficile and Blastocystis
Cited by: 15
Author(s): Laura Vega, Giovanny Herrera, Marina Muñoz, Manuel A. Patarroyo, Jenny G. Maloney, Mónica Santı́n, Juan David Ramírez
Software Mentions: 14
Published: almost 4 years ago

10.1371/journal.ppat.1008653

Genome-wide transcriptomics identifies an early preclinical signature of prion infection
Cited by: 39
Author(s): Silvia Sorce, Mario Nuvolone, Giancarlo Russo, Andra Chincisan, Daniel Heinzer, Merve Avar, Manuela Pfammatter, Petra Schwarz, Mirzet Delic, Mattia Müller, Simone Hornemann, Despina Sanoudou, Claudia Scheckel, Adriano Aguzzi
Software Mentions: 14
Published: over 4 years ago

10.1016/j.celrep.2019.06.037

Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis
Cited by: 99
Author(s): Covadonga Vara, Andreu Paytuví-Gallart, Yasmina Cuartero, François Le Dily, Francisca García, Judit Salvà-Castro, Laura Gómez-H, Eva Julià, Cátia Moutinho, Riccardo Aiese Cigliano, Walter Sanseverino, Òscar Fornas, Alberto M. Pendás, Holger Heyn, Paul D. Waters, Marc A. Martí‐Renom, Aurora Ruiz‐Herrera
Software Mentions: 14
Published: over 5 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 sequencing
Cited by: 32
Author(s): Zachary D Wallen
Software Mentions: 14
Published: over 3 years ago

10.1186/s40478-020-0880-6

Single-nucleus RNA-seq identifies Huntington disease astrocyte states
Cited by: 147
Author(s): Osama Al‐Dalahmah, Alexander A. Sosunov, Ayesha Shaik, Kenneth Ofori, Yang Liu, Jean Paul Vonsattel, István Adorján, Vilas Menon, James E. Goldman
Software Mentions: 14
Published: almost 5 years ago

10.3389/fmicb.2021.709611

Breeding Strategy Shapes the Composition of Bacterial Communities in Female Nile Tilapia Reared in a Recirculating Aquaculture System
Cited by: 2
Author(s): Yousri Abdelhafiz, Jorge M. O. Fernandes, Simone Larger, Davide Albanese, Claudio Donati, Omid Jafari, Artem Nedoluzhko, Viswanath Kiron
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 data
Cited by: 650
Author(s): Xijin Ge, Eun Wo Son, Runan Yao
Software Mentions: 14
Published: about 6 years ago

10.1038/s41396-020-00798-6

Mucin-derived O-glycans supplemented to diet mitigate diverse microbiota perturbations
Cited by: 48
Author(s): Kali M. Pruss, Ángela Marcobal, Audrey Southwick, Dylan Dahan, Sam Smits, Jessica A. Ferreyra, Steven K. Higginbottom, Erica D. Sonnenburg, Purna C. Kashyap, Biswa Choudhury, Lars Bode, Justin L. Sonnenburg
Software Mentions: 14
Published: about 4 years ago

10.3390/cancers13174348

Histological Grade of Endometrioid Endometrial Cancer and Relapse Risk Can Be Predicted with Machine Learning from Gene Expression Data
Cited by: 4
Author(s): Péter Gargya, Bálint László Bálint
Software Mentions: 14
Published: over 3 years ago

10.1186/s13148-021-01173-8

Histone H3 lysine 27 acetylation profile undergoes two global shifts in undernourished children and suggests altered one-carbon metabolism
Cited by: 5
Author(s): Kristyna Kupkova, Savera J. Shetty, Rashidul Haque, William A. Petri, David T. Auble
Software Mentions: 14
Published: about 3 years ago

10.3390/microorganisms9061222

Salivary Microbiome Diversity in Kuwaiti Adolescents with Varied Body Mass Index—A Pilot Study
Cited by: 5
Author(s): Hend Alqaderi, Meganathan P. Ramakodi, Rasheeba Nizam, Sindhu Jacob, Sriraman Devarajan, Muthukrishnan Eaaswarkhanth, Fahd Al-Mulla
Software Mentions: 14
Published: over 3 years ago

10.1186/s12920-017-0274-1

Quantitative analysis of cryptic splicing associated with TDP-43 depletion
Cited by: 74
Author(s): Jack Humphrey, Warren Emmett, Pietro Fratta, Adrian M. Isaacs, Vincent Plagnol
Software Mentions: 14
Published: over 7 years ago

10.1002/1873-3468.12684

Computational approaches for interpreting sc <scp>RNA</scp> ‐seq data
Cited by: 111
Author(s): Raghd Rostom, Valentine Svensson, Sarah A. Teichmann, Gozde Kar
Software Mentions: 14
Published: over 7 years ago

10.3389/fonc.2020.575422

A Novel Model Based on CXCL8-Derived Radiomics for Prognosis Prediction in Colorectal Cancer
Cited by: 8
Author(s): Yanpeng Chu, Jie Li, Zong Yuan Zeng, Bin Huang, Jiaojiao Zhao, Qin Liu, Huaping Wu, Jiangping Fu, Zheng Yin, Yefan Zhang, Jianqiang Cai, Fanxin Zeng
Software Mentions: 14
Published: about 4 years ago

10.3389/fimmu.2021.557994

Investigation of Genetic Determinants of Glioma Immune Phenotype by Integrative Immunogenomic Scale Analysis
Cited by: 10
Author(s): Binghao Zhao, Yuekun Wang, Yaning Wang, Congxin Dai
Software Mentions: 14
Published: over 3 years ago

10.12688/f1000research.24956.2

gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler
Cited by: 274
Author(s): Liis Kolberg, Uku Raudvere, Ivan Kuzmin, Jaak Vilo, Hedi Peterson
Software Mentions: 14
Published: about 4 years ago

10.12688/f1000research.12223.1

recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor
Cited by: 47
Author(s): Leonardo Collado‐Torres, Abhinav Nellore, Andrew E. Jaffe
Software Mentions: 14
Published: over 7 years ago

10.3389/fgene.2021.689406

Reference Transcriptomes of Porcine Peripheral Immune Cells Created Through Bulk and Single-Cell RNA Sequencing
Cited 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

10.1038/s41598-021-97071-3

Characterizing rhizosphere microbiota of peanut (Arachis hypogaea L.) from pre-sowing to post-harvest of crop under field conditions
Cited by: 10
Author(s): Ankit T. Hinsu, Ketankumar Panchal, Ramesh Pandit, Prakash G. Koringa, Ramesh Kothari
Software Mentions: 14
Published: over 3 years ago

10.1186/s13059-018-1484-3

CTCF maintains regulatory homeostasis of cancer pathways
Cited 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: over 6 years ago

10.3389/fgene.2020.522125

Identification of Prognostic Markers in Cholangiocarcinoma Using Altered DNA Methylation and Gene Expression Profiles
Cited 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

10.1186/s13072-020-00342-y

ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation
Cited by: 39
Author(s): Jake J. Reske, Mike R. Wilson, Ronald L. Chandler
Software Mentions: 14
Published: over 4 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

10.1186/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: over 4 years ago

10.12688/f1000research.6379.2

regionReport: Interactive reports for region-level and feature-level genomic analyses
Cited by: 2
Author(s): Leonardo Collado‐Torres, Andrew E. Jaffe, Jeffrey T. Leek
Software Mentions: 13
Published: over 8 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/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: over 3 years ago

Projects: bioconductor: DESeq2

Papers Mentioning DESeq2 9,583