bioconductor: MSnbase | Projects | Ecosyste.ms: Papers

10.3390/metabo9100200

The metaRbolomics Toolbox in Bioconductor and beyond
Cited by: 61
Author(s): Jan Stanstrup, Corey D. Broeckling, Rick Helmus, Nils Hoffmann, Ewy A. Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Michael Rainer, Reza M. Salek, Tobias Schulze, Emma L. Schymanski, Michael A. Stravs, Etienne Thévenot, Hendrik Treutler, Ralf Weber, Egon Willighagen, Michael Witting, Steffen Neumann
Software Mentions: 92
Published: about 5 years ago

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

10.3390/ijms22063251

Untargeted In Silico Compound Classification—A Novel Metabolomics Method to Assess the Chemodiversity in Bryophytes
Cited by: 11
Author(s): Kristian Peters, Gerd Ulrich Balcke, Niklas Kleinenkuhnen, Hendrik Treutler, Steffen Neumann
Software Mentions: 31
Published: almost 4 years ago

10.3390/metabo9100222

Chemical Diversity and Classification of Secondary Metabolites in Nine Bryophyte Species
Cited by: 29
Author(s): Kristian Peters, Hendrik Treutler, Stefanie Döll, Alida Kindt, Thomas Hankemeier, Steffen Neumann
Software Mentions: 15
Published: about 5 years ago

10.1371/journal.pone.0256016

Integration of chronological omics data reveals mitochondrial regulatory mechanisms during the development of hepatocellular carcinoma
Cited by: 2
Author(s): J. Noé García-Chávez, Verónica Rocío Vásquez-Garzón, Mercedes G. López, Saúl Villa‐Treviño, Rafaél Montiel
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pcbi.1009148

POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis
Cited by: 12
Author(s): Pol Castellano‐Escuder, Raúl González‐Domínguez, Francesc Carmona-Pontaque, Cristina Andrés‐Lacueva, Álex Sánchez-Pla
Software Mentions: 8
Published: over 3 years ago

10.1186/1756-0500-5-360

LXtoo: an integrated live Linux distribution for the bioinformatics community
Cited by: 5
Author(s): Guangchuang Yu, Li-Gen Wang, Xiaohong Meng, Qing-Yu He
Software Mentions: 7
Published: over 12 years ago

10.7554/eLife.65557

Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing in Drosophila
Cited by: 24
Author(s): Evelyn L Eastwood, Kayla A Jara, Susanne Bornelöv, Marzia Munafò, Vasileios Frantzis, Emma Kneuss, Elisar Barbar, Benjamin Czech, Gregory J. Hannon
Software Mentions: 6
Published: almost 4 years ago

10.3390/ijms22094598

Combined Transcriptomic and Proteomic Analysis of Perk Toxicity Pathways
Cited by: 6
Author(s): Rebeka Popovic, Ivana Celardo, Yao Yu, Ana Carolina Oliveira Costa, Samantha H. Y. Loh, L. Miguel Martins
Software Mentions: 6
Published: over 3 years ago

10.1016/j.celrep.2019.11.026

Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome
Cited by: 53
Author(s): Edward Lau, Yu Han, Damon R. Williams, Cody T Thomas, Rajani Shrestha, Joseph C. Wu, Maggie Lam
Software Mentions: 6
Published: about 5 years ago

10.1186/s12915-018-0547-y

Species comparison of liver proteomes reveals links to naked mole-rat longevity and human aging
Cited by: 52
Author(s): Ivonne Heinze, Martin Bens, Enrico Calzia, Susanne Holtze, Oleksandr Dakhovnik, Arne Sahm, Joanna Kirkpatrick, Karol Szafranski, Natalie Romanov, Sai Nagender Sama, Kerstin Hölzer, Stephan Singer, Maria A. Ermolaeva, Matthias Platzer, Thomas B. Hildebrandt, Alessandro Ori
Software Mentions: 6
Published: over 6 years ago

10.15252/msb.20177608

Landscape of nuclear transport receptor cargo specificity
Cited by: 79
Author(s): Marie‐Therese Mackmull, Bernd Klaus, Ivonne Heinze, Manopriya Chokkalingam, Andreas Beyer, Robert B. Russell, Alessandro Ori, Martin Beck
Software Mentions: 5
Published: about 7 years ago

10.12688/f1000research.10411.2

A Bioconductor workflow for processing and analysing spatial proteomics data
Cited by: 23
Author(s): Lisa M. Breckels, Claire M. Mulvey, Kathryn S. Lilley, Laurent Gatto
Software Mentions: 5
Published: over 6 years ago

10.1093/bioinformatics/btz160

Interoperable and scalable data analysis with microservices: applications in metabolomics
Cited by: 24
Author(s): Payam Emami Khoonsari, Pablo Moreno-Ger, Sven Bergmann, Joachim Burman, Marco Capuccini, Matteo Carone, Marta Cascante, Pedro de Atauri, Carles Foguet, Alejandra N. González-Beltrán, Thomas Hankemeier, Kenneth Haug, Sijin He, Stephanie Herman, David Johnson, Namrata Kale, Anders Larsson, Steffen Neumann, Kristian Peters, Luca Pireddu, Philippe Rocca-Serra, Pierrick Roger, Rico Rueedi, Christoph Ruttkies, Noureddin Sadawi, Reza M. Salek, Susanna-Assunta Sansone, Daniel Schober, Vitaly A. Selivanov, Etienne Thévenot, Michael Van Vliet, Gianluigi Zanetti, Christoph Steinbeck, Kim Kultima, Ola Spjuth
Software Mentions: 4
Published: almost 6 years ago

10.1074/mcp.RA117.000189

Spatial Tissue Proteomics Quantifies Inter- and Intratumor Heterogeneity in Hepatocellular Carcinoma (HCC)
Cited by: 63
Author(s): Katarzyna Buczak, Alessandro Ori, Joanna Kirkpatrick, Kerstin Hölzer, Daniel Dauch, Stephanie Roessler, Volker Endris, Felix Lasitschka, Luca Parca, Alexander Schmidt, Lars Zender, Peter Schirmacher, Jeroen Krijgsveld, Stephan Singer, Martin Beck
Software Mentions: 4
Published: over 6 years ago

10.1093/bioinformatics/btw580

DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics
Cited by: 212
Author(s): Samuel Wieczorek, Florence Combes, Cosmin Lazar, Quentin Giai Gianetto, Laurent Guy, Alexia Dorffer, Anne-Marie Hesse, Yohann Couté, Myriam Ferro, Christophe Bruley, Thomas Bürger
Software Mentions: 4
Published: over 8 years ago

10.1038/s41597-020-0499-2

High-throughput transcriptomic and proteomic profiling of mesenchymal-amoeboid transition in 3D collagen
Cited by: 13
Author(s): Vladimı́r Čermák, Aneta Gandalovičová, Ladislav Merta, Karel Harant, Daniel Rösel, Jan Brábek
Software Mentions: 4
Published: over 4 years ago

10.1093/bioinformatics/btv146

Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments
Cited by: 186
Author(s): Kyle D. Bemis, April Harry, Lívia S. Eberlin, Christina R. Ferreira, Stephanie M. W. Y. van de Ven, Parag Mallick, Mark L. Stolowitz, Olga Vitek
Software Mentions: 3
Published: almost 10 years ago

10.1016/j.chom.2020.09.011

A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions
Cited by: 169
Author(s): Konstantin Barylyuk, Luděk Kořený, Huiling Ke, Simon Butterworth, Oliver M. Crook, Imen Lassadi, Vipul Gupta, Eelco C. Tromer, Tobias Mourier, Tim J. Stevens, Lisa M. Breckels, Arnab Pain, Kathryn S. Lilley, Ross F. Waller
Software Mentions: 3
Published: about 4 years ago

10.12688/f1000research.18636.1

A Bioconductor workflow for the Bayesian analysis of spatial proteomics
Cited by: 23
Author(s): Oliver M. Crook, Lisa M. Breckels, Kathryn S. Lilley, Paul Kirk, Laurent Gatto
Software Mentions: 2
Published: over 5 years ago

10.1093/bioinformatics/btu013

Mass-spectrometry-based spatial proteomics data analysis using <tt>pRoloc</tt> and <tt>pRolocdata</tt>
Cited by: 80
Author(s): Laurent Gatto, Lisa M. Breckels, Samuel Wieczorek, Thomas Bürger, Kathryn S. Lilley
Software Mentions: 2
Published: almost 11 years ago

10.3390/metabo11060400

A Compositional Model to Predict the Aggregated Isotope Distribution for Average DNA and RNA Oligonucleotides
Cited by: 1
Author(s): Annelies Agten, Piotr Prostko, Melvin Geubbelmans, Youzhong Liu, Thomas De Vijlder, Dirk Valkenborg
Software Mentions: 2
Published: over 3 years ago

10.3390/metabo10080301

Comprehensive Vitamer Profiling of Folate Mono- and Polyglutamates in Baker’s Yeast (Saccharomyces cerevisiae) as a Function of Different Sample Preparation Procedures
Cited by: 6
Author(s): Lena Gmelch, Daniela Wirtz, Michael Witting, Nadine Weber, Lisa Striegel, Philippe Schmitt‐Kopplin, Michael Rychlik
Software Mentions: 1
Published: over 4 years ago

10.1111/acel.13342

HLH‐30‐dependent rewiring of metabolism during starvation in C . elegans
Cited by: 4
Author(s): Kathrine B. Dall, Jesper Foged Havelund, Eva Bang Harvald, Michael Witting, Nils J. Færgeman
Software Mentions: 1
Published: almost 4 years ago

Ecosyste.ms: Papers

Projects: bioconductor: MSnbase

Papers Mentioning MSnbase 24