Data Analysis

BigPint Bioconductor package that makes BIG (RNA seq) data pint sized

The BigPint package can help examine any large multivariate dataset. However, we note that the example datasets and example code in this package consider RNA-sequencing datasets. If you are using this software for RNA-sequencing data, then it can help you confirm that the variability between your treatment groups is larger than that between your replicates and determine how various normalization techniques in popular RNA-sequencing analysis packages (such as edgeR, DESeq2, and limma) affect your dataset.

CLIJ2

CLIJ2 is a GPU-accelerated image processing library for ImageJ/Fiji, Icy, Matlab and Java based on OpenCL. It comes with hundreds of operations for filtering, binarizing, labeling, measuring in images, projections, transformations and mathematical operations for images.

morphologica

morphologica is a header-only C++ library which provides simulation support facilities for simulations of dynamical systems. It helps with: Configuration: morphologica allows you to easily set up a simulation parameter configuration system, using the JSON reading and writing abilities of morph::Config.

NetPyNE

NetPyNE (Networks using Python and NEURON) is a Python package to facilitate the development, simulation, parallelization, analysis, and optimization of biophysical neuronal networks using the NEURON simulator. For more details, installation instructions, documentation, tutorials, forums, videos and more, please visit: www.

Collaborative Informatics and Neuroimaging Suite Toolkit for Anonymous Computation (COINSTAC)

COINSTAC provides a platform to analyze data stored locally across multiple organizations without the need for pooling the data at any point during the analysis. It is intended to be an ultimate one-stop shop by which researchers can build any statistical or machine learning model collaboratively in a decentralized fashion.

Greedy

Greedy is a tool for fast medical image registration. It is a fast CPU-based deformable image registration tool that can be used in applications where many images have to be registered in parallel.

ERPLAB

ERPLAB Toolbox is a free, open-source Matlab package for analyzing ERP data. It is tightly integrated with EEGLAB Toolbox, extending EEGLAB’s capabilities to provide robust, industrial-strength tools for ERP processing, visualization, and analysis.

TGAC Browser

The TGAC Browser is a Genomic Browser with novel rendering and annotation capabilities designed to overcome some shortcomings in available approaches. It was developed to visualize genome annotations from Ensembl Database Schema.

BrainSMASH

BrainSMASH is a Python-based framework for quantifying the significance of a brain map’s spatial topography in studies of large-scale brain organization. BrainSMASH was designed to generate synthetic brain maps with spatial autocorrelation (SA) matched to the SA of a target brain map.

FastTrack

FastTrack is an open-source cross-platform tracking software. Easy to install and easy to use, it can track a large variety of systems from active particles to animals, with a known or unknown number of objects.