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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... -
Bioalerts: a python library for the derivation of structural alerts from bioa...
Background Assessing compound toxicity at early stages of the drug discovery process is a crucial task to dismiss drug candidates likely to fail in clinical trials. Screening... -
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... -
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... -
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,... -
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... -
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... -
"A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative pro...
Background Comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach... -
TCGA2BED: Extracting, extending, integrating, and querying The Cancer Genome ...
Background Data extraction and integration methods are becoming essential to effectively access and take advantage of the huge amounts of heterogeneous genomics and clinical... -
SoftPanel: a website for grouping diseases and related disorders for generati...
Background Targeted next-generation sequencing is playing an increasingly important role in biological research and clinical diagnosis by allowing researchers to sequence high... -
CytoSpectre: a tool for spectral analysis of oriented structures on cellular ...
Background Orientation and the degree of isotropy are important in many biological systems such as the sarcomeres of cardiomyocytes and other fibrillar structures of the... -
ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publica...
Background Next generation sequencing (NGS) technologies enable studies and analyses of the diversity of both T and B cell receptors (TCR and BCR) in human and animal systems to... -
"CellProfiler Tracer: exploring and validating high-throughput, time-lapse mi...
Background Time-lapse analysis of cellular images is an important and growing need in biology. Algorithms for cell tracking are widely available; what researchers have been... -
Fostering serendipitous knowledge discovery using an adaptive multigraph-base...
Serendipity, the art of making an unsought finding plays also an important role in the emerging field of data science, allowing the discovery of interesting and valuable facts...
