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.

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.

INCF Portal

The INCF portal is the guide to the INCF activities and its community resources. INCF advances data reuse and reproducibility in brain research by coordinating the development of Open, FAIR, and Citable tools and resources for neuroscience

Open Source Brain

Open Source Brain, a platform for sharing, viewing, analyzing, and simulating standardized models from different brain regions and species. Model structure and parameters can be automatically visualized and their dynamical properties explored through browser-based simulations.

MorphoPy: A python package for feature extraction of neural morphologies

MorphoPy is an open software package written in Python3 that allows for visualization and processing of morphological reconstructions of neural data. It has been created to facilitate the translation from morphology graphs into descriptive features like density maps, morphometric statistics, and persistence diagrams for down-stream exploration and statistical analysis.

OpenCitations

OpenCitations is an independent infrastructure organization for open scholarship dedicated to the publication of open bibliographic and citation data by the use of Semantic Web (Linked Data) technologies. It is also engaged in advocacy for open citations, particularly by organizing the Workshops for Open Citations and Scholarly Metadata, and in its role as a key founding member of the Initiative for Open Citations (I4OC) and the Initiative for Open Abstracts (I4OA).

DIPY

DIPY is the paragon 3D/4D+ imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.