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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version.
Proper citation: BECA (RRID:SCR_015846) Copy
Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
Proper citation: Avogadro (RRID:SCR_015983) Copy
https://github.com/brain-life/encode
Software that implements a framework to encode structural brain connectomes into multidimensional arrays (tensors). Encoding Connectomes provides an agile framework for computing over connectome edges and nodes.
Proper citation: Linear Fascicle Evaluation (RRID:SCR_016153) Copy
Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning.
Proper citation: HyPhy (RRID:SCR_016162) Copy
http://www.nitrc.org/projects/psc/
Data analysis software that can simultaneously characterize a large number of white matter bundles within and across different subjects for group analysis. It has three major components: construction of the structural connectome for the whole brain, low-dimensional representation of streamlines in each connection, and multi-level connectome analysis.
Proper citation: Mapping Population-based Structural Connectomes (RRID:SCR_016232) Copy
Standard specification for organizing and describing outputs of neuroimaging experiments. Used to organize and describe neuroimaging and behavioral data by neuroscientific community as standard to organize and share data. BIDS prescribes file naming conventions and folder structure to store data in set of already existing file formats. Provides standardized templates to store associated metadata in form of Javascript Object Notation (JSON) and tab-separated value (TSV) files. Facilitates data sharing, metadata querying, and enables automatic data analysis pipelines. System to curate, aggregate, and annotate neuroimaging databases. Intended for magnetic resonance imaging data, magnetoencephalography data, electroencephalography data, and intracranial encephalography data.
Proper citation: Brain Imaging Data Structure (BIDs) (RRID:SCR_016124) Copy
Software toolkit for neuroelectrophysiology object modeling and data analysis in Python. Open source Python package for analysis of neuroelectrophysiology data.
Proper citation: nelpy (RRID:SCR_016209) Copy
https://github.com/ihmwg/IHM-dictionary
Software resource for a data representation for integrative/hybrid methods of modeling macromolecular structures.
Proper citation: IHM-dictionary (RRID:SCR_016186) Copy
Data repository for integrative/hybrid structural models of macromolecules and their assemblies. This includes atomistic models as well as multi-scale models consisting of different coarse-grained representations.
Proper citation: PDB-Dev (RRID:SCR_016185) Copy
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001096/
Software pipeline to identify MITEs as well as other small Class 2 non autonomous Transposable Elements from genomic DNA data sets. Used for discovering miniature inverted repeat transposable elements from genomic sequences. Can search large genomic data sets including whole genome sequences.
Proper citation: MITE-Hunter (RRID:SCR_020946) Copy
https://github.com/pyranges/ncls
Software library for nested containment list data structure for interval overlap queries, like interval tree. It is a static interval-tree that is fast for both construction and lookups.
Proper citation: Nested containment list (RRID:SCR_027849) Copy
https://github.com/nlm-irp-jianglab/SpikeHunter
Software deep learning tool for identifying phage tailspike proteins. Used to identify phage tailspike proteins.
Proper citation: SpikeHunter (RRID:SCR_024831) Copy
https://github.com/xinhe-lab/GSFA
Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data.
Proper citation: Guided Sparse Factor Analysis (RRID:SCR_025023) Copy
Software tool for analysis of non-covalent interactions in molecular dynamics trajectories. Implemented in Python and is universally applicable to any kind of MD trajectory supported by MDAnalysis package.
Proper citation: PyContact (RRID:SCR_025066) Copy
Open access knowledge base for microbial natural products discovery. Database of microbially derived natural product structures. Provides coverage of bacterial and fungal natural products to visualize chemical diversity. Includes compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. Interactive web portal permits searching by structure, substructure, and physical properties. Provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. Atlas has been developed under FAIR principles.
Proper citation: Natural Products Atlas (RRID:SCR_025107) Copy
https://github.com/PhysiCell-Tools/PhysiCell-Studio
Software graphical tool to allow easy editing of (XML) model, create initial positions of cells, run simulation, and visualize results. To contribute, fork and make PRs to the development branch. Used to create, execute, and visualize multicellular model using PhysiCell.
Proper citation: PhysiCell Studio (RRID:SCR_025311) Copy
https://github.com/COMBINE-lab/maximum-likelihood-relatedness-estimation
C++ program to infer biological relatedness from low coverage 2nd generation sequencing data. It uses information from genotype likelihoods rather than observed genotypes in maximum likelihood framework in order to estimate the overall coefficient of relatedness as well as individual kinship components between two samples. Maximum Likelihood Estimation of Biological Relatedness from Low Coverage Sequencing Data.
Proper citation: lcMLkin (RRID:SCR_025418) Copy
https://github.com/compgenomics/MeTPeak
Software package for finding the location of m6A sites in MeRIP-seq data.
Proper citation: MeTPeak (RRID:SCR_026533) Copy
https://github.com/YuningHao/FARDEEP
Software R tool for enumerating immune cell subsets from whole tumor tissue samples. Utilizes adaptive least trimmed square to automatically detect and remove outliers before estimating cell compositions.
Proper citation: FARDEEP (RRID:SCR_026704) Copy
https://github.com/DerrickWood/kraken2
Software tool as second version of Kraken taxonomic sequence classification system.
Proper citation: kraken2 (RRID:SCR_026838) Copy
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