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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... -
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... -
BAMQL: a query language for extracting reads from BAM files
Background It is extremely common to need to select a subset of reads from a BAM file based on their specific properties. Typically, a user unpacks the BAM file to a text stream... -
SCNS: a graphical tool for reconstructing executable regulatory networks from...
Background Reconstruction of executable mechanistic models from single-cell gene expression data represents a powerful approach to understanding developmental and disease... -
phylotree.js - a JavaScript library for application development and interacti...
Background While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks... -
G-DOC Plus – an integrative bioinformatics platform for precision medicine
Background G-DOC Plus is a data integration and bioinformatics platform that uses cloud computing and other advanced computational tools to handle a variety of biomedical BIG... -
Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data
Background Somatic copy number alterations (CNAs) contribute to the clinically targetable aberrations in the tumor genome. For both routine diagnostics and biomarkers research,... -
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... -
Canary: an atomic pipeline for clinical amplicon assays
Background High throughput sequencing requires bioinformatics pipelines to process large volumes of data into meaningful variants that can be translated into a clinical report.... -
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular i...
[Background]: Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively... -
ImageJ2: ImageJ for the next generation of scientific image data
Background ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in... -
SG-ADVISER mtDNA: a web server for mitochondrial DNA annotation with data fro...
Background Whole genome and exome sequencing usually include reads containing mitochondrial DNA (mtDNA). Yet, state-of-the-art pipelines and services for human nuclear genome... -
VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient...
Background RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and cells.... -
ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis p...
Background: Transcription factor binding, histone modification, and chromatin accessibility studies are important approaches to understanding the biology of gene regulation.... -
ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gen...
This work was supported through providing funds by the Biotechnology and Biological Sciences Research Council [BB/F005806/1, BB/F005237/1]; and the Engineering and Physical... -
MetaComp: comprehensive analysis software for comparative meta-omics includin...
Background During the past decade, the development of high throughput nucleic sequencing and mass spectrometry analysis techniques have enabled the characterization of microbial... -
CEMiTool: a Bioconductor package for performing comprehensive modular co-expr...
Background The analysis of modular gene co-expression networks is a well-established method commonly used for discovering the systems-level functionality of genes. In addition,... -
MARV: a tool for genome-wide multi-phenotype analysis of rare variants
Background Genome-wide association studies have enabled identification of thousands of loci for hundreds of traits. Yet, for most human traits a substantial part of the... -
Biotite: a unifying open source computational biology framework in Python
Background As molecular biology is creating an increasing amount of sequence and structure data, the multitude of software to analyze this data is also rising. Most of the... -
PanoromiX: a time-course network medicine platform integrating molecular assa...
Background Network medicine aims to map molecular perturbations of any given diseases onto complex networks with functional interdependencies that underlie a pathological...
