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Drug voyager: a computational platform for exploring unintended drug action
Abstract Background The dominant paradigm in understanding drug action focuses on the intended therapeutic effects and frequent... -
DMDtoolkit: a tool for visualizing the mutated dystrophin protein and predict...
Background Dystrophinopathy is one of the most common human monogenic diseases which results in Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD). Mutations... -
metaX: a flexible and comprehensive software for processing metabolomics data
Background Non-targeted metabolomics based on mass spectrometry enables high-throughput profiling of the metabolites in a biological sample. The large amount of data generated... -
NEAT: a framework for building fully automated NGS pipelines and analyses
Background: The analysis of next generation sequencing (NGS) has become a standard task for many laboratories in the life sciences. Though there exists several tools to support... -
gtrellis: an R/Bioconductor package for making genome-level Trellis graphics
Background Trellis graphics are a visualization method that splits data by one or more categorical variables and displays subsets of the data in a grid of panels. Trellis... -
Assessment of k-mer spectrum applicability for metagenomic dissimilarity anal...
Background A rapidly increasing flow of genomic data requires the development of efficient methods for obtaining its compact representation. Feature extraction facilitates... -
Context-specific functional module based drug efficacy prediction
Background It is necessary to evaluate the efficacy of individual drugs on patients to realize personalized medicine. Testing drugs on patients in clinical trial is the only way... -
MultiDataSet: an R package for encapsulating multiple data sets with applicat...
BACKGROUND: Reduction in the cost of genomic assays has generated large amounts of biomedical-related data. As a result, current studies perform multiple experiments in the same... -
Risk-conscious correction of batch effects: maximising information extraction...
Background Batch effects are a persistent and pervasive form of measurement noise which undermine the scientific utility of high-throughput genomic datasets. At their most... -
Roar: detecting alternative polyadenylation with standard mRNA sequencing lib...
Background Post-transcriptional regulation is a complex mechanism that plays a central role in defining multiple cellular identities starting from a common genome. Modifications... -
ClinQC: a tool for quality control and cleaning of Sanger and NGS data in cli...
Background Traditional Sanger sequencing has been used as a gold standard method for genetic testing in clinic to perform single gene test, which has been a cumbersome and... -
From raw data to data-analysis for magnetic resonance spectroscopy – the miss...
Background Magnetic resonance spectroscopy provides metabolic information about living tissues in a non-invasive way. However, there are only few multi-centre clinical studies,... -
Tilting the Lasso by Knowledge-Based Post-Processing
Background It is useful to incorporate biological knowledge on the role of genetic determinants in predicting an outcome. It is, however, not always feasible to fully elicit... -
msBiodat analysis tool, big data analysis for high-throughput experiments
Background Mass spectrometry (MS) are a group of a high-throughput techniques used to increase knowledge about biomolecules. They produce a large amount of data which is... -
"A scalability study of phylogenetic network inference methods using empirica...
Background Branching events in phylogenetic trees reflect bifurcating and/or multifurcating speciation and splitting events. In the presence of gene flow, a phylogeny cannot be... -
Finding and sharing GIS methods based on the questions they answer
Geographic information has become central for data scientists of many disciplines to put their analyzes into a spatio-temporal perspective. However, just as the volume and... -
Cnidaria: fast, reference-free clustering of raw and assembled genome and tra...
Background: Identification of biological specimens is a major requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying... -
Je, a versatile suite to handle multiplexed NGS libraries with unique molecul...
Background The yield obtained from next generation sequencers has increased almost exponentially in recent years, making sample multiplexing common practice. While barcodes... -
RGmatch: matching genomic regions to proximal genes in omics data integration
© The Author(s). 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License... -
DensityMap: a genome viewer for illustrating the densities of features
Background Several tools are available for visualizing genomic data. Some, such as Gbrowse and Jbrowse, are very efficient for small genomic regions, but they are not suitable...
