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(Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.
an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.
is a command-line tool for converting 3D images between common file formats.
a comprehensive and integrative circular RNA analysis toolset.
a software package for visualizing data and information. It visualizes data in a circular layout.
Keywords:
Visualization
(Computational Radiology Kit) a collection of algorithms and image processing tools developed by the Computational Radiology Laboratory team.
a software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
DCMTK is a collection of libraries and applications implementing large parts the DICOM standard.
enables fast and sensitive comparisons of large structure sets.
Grassroots DiCoM is a C++ library for DICOM medical files. It is accessible from Python, C#, Java and PHP.
a free tool offered by Golden Helix that delivers stunning visualizations of your genomic data, enabling you to see what is occurring at each base pair in your samples.
Automated brain extraction of multi-sequence MRI using artificial neural networks.
(Integrative Genomics Viewer) a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
Creates self-contained html pages for visual variant review with IGV (igv.js).
An open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images
(Insight Toolkit) is an open-source, cross-platform library that provides developers with an extensive suite of software tools for image analysis
is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
is a cross-platform NIfTI format image viewer. It can load multiple layers of images, generate volume renderings and draw volumes of interest. It also provides dcm2nii for converting DICOM images to NIfTI format and NPM for statistics. MRIcron is a mature and useful tool, however you may want to consider the more recent MRIcroGL as an alternative.
provides a set of tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses.
contains programs to perform EM based segmentation of images in nifti or analyse format.
a trainable, memory-efficient, and GPU-friendly PyTorch reproduction of DeepMind's AlphaFold 2.
open source version of the widely used molecular visualization package developed by Warren DeLano.
(Robust Brain Extraction) is an automatic whole-brain extraction tool for T1-weighted MRI data (commonly known as skull stripping).
is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.
(SAM) produces high quality object masks from input prompts such as points or boxes, and it can be used to generate masks for all objects in an image.
a Bioconductor software package installed in R 3.2.2 that takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo.
provides analysis and publication quality printing of linear and circular RNA splicing, expression and regulation.
Software Introduction SPM is made freely available to the [neuro]imaging community, to promote collaboration and a common analysis scheme across laboratories. The software represents the implementation of the theoretical concepts of Statistical Parametric Mapping in a complete analysis package. The SPM software is a suite of MATLAB (MathWorks) functions and subroutines with some externally compiled C routines. SPM was written to organise and interpret …
tool for fast and accurate white matter bundle segmentation from Diffusion MRI. It can create bundle segmentations, segmentations of the endregions of bundles and Tract Orientation Maps (TOMs). Moreover, it can do tracking on the TOMs creating bundle-specific tractogram and do Tractometry analysis on those.
Plotting of aligned sequencing reads, assembled contigs or pan-genome graphs in BAM/CRAM/GFA format and visualization of genomic variants.
command line tools for sequence logo generation.
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