preciseTAD provides functions to predict the location of boundaries of topologically associated domains (TADs) and chromatin loops at base-level resolution.
OpenStructure is an open-source computational structural biology framework.This project aims to provide an open-source, modular, flexible, molecular modelling and visualization environment. It is targeted at interested method developers in the field of structural bioinformatics.
OpenMS is an open-source software C++ library for LC/MS data management and analyses. It offers an infrastructure for the development of mass spectrometry related software.
pyOpenMS provides Python-bindings for the C++ OpenMS mass spectrometric algorithm library, allowing researchers to directly access algorithms and data structures available in C++ from the interactive Python environment. pyOpenMS thus provides access to a feature-rich, open-source algorithm library for mass-spectrometry based proteomics analysis, giving the user functionality ranging from file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ and SWATH analysis tools).
ALF simulates a wide range of evolutionary forces that act on genomes, such as character substitutions, indels, gene duplication, gene loss, lateral gene transfer and genome rearrangement.
Frida (FRamework for Image Dataset Analysis) is image analysis software. Frida was developed by the Johns Hopkins University Tissue Microarray Core Facility. Frida is open source and written in 100% Java. Frida makes use of functionality from the NIH’s ImageJ application.
Cornish T, Morgan J, Gurel B, and De Marzo AM.
FrIDA: An open source framework for image dataset analysis.
Arch. Pathol. Lab. Med. 132:856 (2008). Originally presented at Advancing Practice, Instruction and Innovation Through Informatics: Pittsburgh, PA, 2007.
Neji is a innovative and powerfull framework for faster biomedical concept recognition. It is open source and built around four key characteristics: modularity, scalability, speed, and usability. Neji integrates modules of various state-of-the-art methods for biomedical natural language processing (e.g., sentence splitting, tokenization, lemmatization, part-of-speech tagging, chunking and dependency parsing) and concept recognition (e.g., dictionaries and machine learning). The most popular input and output formats, such as Pubmed XML, IeXML, CoNLL and A1, are also supported.
ABrowse is an open source genome browser framework for not only end users, but also data providers and developers. Powered by cutting-edge technologies, ABrowse provides a rather comprehensive set of features as a modern next-generation genome browser framework
DNENRICH is a statistical software package for calculating gene set enrichment for de novo mutations (typically detected by exome sequencing) of a disease cohort.
