Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments

Bioinformatics
Kyle D BemisOlga Vitek

Abstract

Cardinal is an R package for statistical analysis of mass spectrometry-based imaging (MSI) experiments of biological samples such as tissues. Cardinal supports both Matrix-Assisted Laser Desorption/Ionization (MALDI) and Desorption Electrospray Ionization-based MSI workflows, and experiments with multiple tissues and complex designs. The main analytical functionalities include (1) image segmentation, which partitions a tissue into regions of homogeneous chemical composition, selects the number of segments and the subset of informative ions, and characterizes the associated uncertainty and (2) image classification, which assigns locations on the tissue to pre-defined classes, selects the subset of informative ions, and estimates the resulting classification error by (cross-) validation. The statistical methods are based on mixture modeling and regularization.

References

Feb 16, 2011·Journal of Mass Spectrometry : JMS·Jeramie D WatrousPieter C Dorrestein

❮ Previous
Next ❯

Citations

Nov 28, 2015·Metabolomics : Official Journal of the Metabolomic Society·Philippe Rocca-SerraSteffen Neumann
Aug 26, 2016·Analytical Chemistry·Alan M RaceJosephine Bunch
Nov 15, 2016·Scientific Reports·Nathan Heath PattersonPeter Metrakos
Mar 17, 2017·Biochimica Et Biophysica Acta. General Subjects·Jusal QuanicoIsabelle Fournier
Apr 4, 2017·Bioinformatics·Pere RàfolsXavier Correig
Jul 25, 2018·Journal of Neurochemistry·Wojciech MichnoJörg Hanrieder
May 1, 2019·Journal of Mass Spectrometry : JMS·Ethan YangPierre Chaurand
Nov 22, 2018·ILAR Journal·Lauren E HimmelKelli L Boyd
Aug 1, 2019·Natural Product Reports·Joseph E SprakerLaura M Sanchez
May 1, 2019·Analytical and Bioanalytical Chemistry·Christina MeisenbichlerThomas Müller
Nov 12, 2015·Clinical Chemistry·Demian R Ifa, Livia S Eberlin
Oct 12, 2019·Mass Spectrometry Reviews·Nico VerbeeckRaf Van de Plas
Aug 15, 2019·Journal of Mass Spectrometry : JMS·Ethan YangPierre Chaurand
Jun 18, 2017·Electrophoresis·Biswapriya B MisraDmitry Grapov
Mar 21, 2018·International Journal of Legal Medicine·Aleksandra AljaknaAurélien Thomas
Jun 26, 2020·Journal of Personalized Medicine·Eline BerghmansGeert Baggerman
Feb 6, 2020·Nature Microbiology·Benedikt GeierManuel Liebeke
Mar 23, 2019·Cell Biology and Toxicology·Jeovanis GilGyörgy Marko-Varga
Dec 10, 2019·GigaScience·Melanie Christine FöllOliver Schilling
Oct 11, 2017·Metabolomics : Official Journal of the Metabolomic Society·Nicholas J BondZoe Hall
Oct 11, 2020·BMC Bioinformatics·Stefania Alexandra IakabPere Ràfols
Oct 21, 2020·Biochemical Society Transactions·Lindsay K PinoBirgit Schilling

❮ Previous
Next ❯

Software Mentioned

MALDIquant
MSnbase
SCiLS
MSiReader
Windows
DataCube Explorer
Cardinal
TissueView
R
SASA

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.