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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.
https://github.com/aplbrain/saber
Library of containerized tools and workflow deployment system for enabling processing of large neuroimaging datasets. Provides canonical neuroimaging workflows specified in standard workflow language (CWL), integration with workflow execution engine (Airflow), imaging database (bossDB), and parameter database (Datajoint) to deploy workflows at scale, and tools to automate deployment and optimization of neuroimaging pipelines.
Proper citation: Scalable Analytics for Brain Exploration Research (RRID:SCR_018812) Copy
https://openwetware.org/wiki/RAVE
Open source software tool for reproducible analysis and visualization of intracranial EEG data. Used for analysis of intracranial electroencephalogram data, including data collected using strips and grids (electrocorticography, ECoG) and depth electrodes (stereotactic EEG).
Proper citation: RAVE (RRID:SCR_019040) Copy
https://github.com/davidaknowles/leafcutter/
Software tool for identifying and quantifying RNA splicing variation. Used to study sample and population variation in intron splicing. Identifies variable intron splicing events from short read RNA-seq data and finds alternative splicing events of high complexity. Used for detecting differential splicing between sample groups, and for mapping splicing quantitative trait loci (sQTLs).
Proper citation: LeafCutter (RRID:SCR_017639) Copy
https://github.com/zburkett/VoICE
Software that groups vocal elements of birdsong by creating a high dimensionality dataset through scoring spectral similarity between vocalizations.
Proper citation: Vocal Inventory Clustering Engine (VoICE) (RRID:SCR_016004) Copy
https://github.com/broadinstitute/Drop-seq
Software Java tools for analyzing Drop-seq data. Used to analyze gene expression from thousands of individual cells simultaneously. Analyzes mRNA transcripts while remembering origin cell transcript.
Proper citation: Drop-seq tools (RRID:SCR_018142) Copy
https://github.com/satijalab/seurat
Software R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. Used for quality control, analysis, and exploration of single-cell RNA sequencing (scRNA-seq) data.
Proper citation: Seurat (RRID:SCR_016341) Copy
Web based tool to visualize gene expression and metadata annotation distribution throughout single cell dataset or multiple datasets. Interactive viewer for single cell expression. You can click on and hover over cells to get meta information, search for genes to color on and click clusters to show cluster specific marker genes.
Proper citation: UCSC Cell Browser (RRID:SCR_023293) Copy
https://www.delaneycare.org/index.php
The Collaboratory of AIDS Researchers for Eradication (CARE) is a consortium of scientific experts in the field of HIV latency from several U.S. and European academic research institutions as well as Merck Research Laboratories working together to find a cure for HIV.
Proper citation: Collaboratory of AIDS Researchers for Eradciation (CARE) (RRID:SCR_013681) Copy
http://hbatlas.org/pages/publications
A research paper with supplementary materials reporting the generation and analysis of exon-level transcriptome and associated genotyping data. The experiment represented both males and females of multiple ethnicities and examines gene regulation and expression in different areas of the brain. A data set on the human brain transcriptome as well as insights into the transcriptional foundations of human neurodevelopment is provided.
Proper citation: Spatio-temporal transcriptome of the human brain (RRID:SCR_013743) Copy
http://www.nitrc.org/projects/nusdast
A repository of schizophrenia neuroimaging data collected from over 450 individuals with schizophrenia, healthy controls and their respective siblings, most with 2-year longitudinal follow-up. The data include neuroimaging data, cognitive data, clinical data, and genetic data.
Proper citation: Northwestern University Schizophrenia Data and Software Tool (NUSDAST) (RRID:SCR_014153) Copy
http://krasnow1.gmu.edu/CENlab/software.html
Stochastic reaction-diffusion simulator in Java which is used for simulating neuronal signaling pathways.
Proper citation: NeuroRD (RRID:SCR_014769) Copy
http://www.open-ephys.org/pulsepal
Open source pulse train generator that allows users to create and trigger software defined trains of voltage pulses with high temporal precision. Generates precisely timed pulse sequences for use in research involving electrophysiology or psychophysics.
Proper citation: Open Ephys: Pulse Pal (RRID:SCR_017203) Copy
http://kim.bio.upenn.edu/software/pivot.shtml
Software R package for interactive analysis and visualization of transcriptomics data. Operating systems are macOS, Linux, Windows.
Proper citation: PIVOT software (RRID:SCR_017210) Copy
http://www.brainimagelibrary.org
Public, NIH-funded repository and analysis ecosystem for brain microscopy data, designed to store, share, and process massive volumetric datasets. It enables researchers to access whole-brain images, neuron morphologies, and spatial data without needing to download, fostering collaborative discovery. Used to deposit, analyze, mine, share and interact with large brain image datasets.
Proper citation: Brain Image Library (RRID:SCR_017272) Copy
BossDB (Brain Observatory Storage Service and Database) is a cloud-based ecosystem for the storage and management of public large-scale volumetric neuroimaging and connectomics datasets. This includes volumetric Electron Microscopy and X-Ray Micro/Nanotomography data with support for multi-channel image data, segmentations, annotations, meshes, and connectomes. BossDB integrates with community resources for data access, processing, visualization, and analysis, and includes an API that enables metadata management, rendering, datatype conversions, and ingest.
Proper citation: Brain Observatory Storage Service and Database (BossDB) (RRID:SCR_017273) Copy
https://github.com/SciCrunch/NIF-Ontology/tree/neurons/ttl
An ontology for describing the complex phenotypes of neurons.
Proper citation: Neuron Phenotype Ontology (RRID:SCR_017403) Copy
Portal for visualization and analysis of multi omic data in public and private domains. Enables upload, visualization and analysis of scRNA-seq data.
Proper citation: gene Expression Analysis Resource (RRID:SCR_017467) Copy
https://github.com/PriceLab/TReNA
Methods for reconstructing transcriptional regulatory networks.
Proper citation: TReNA (RRID:SCR_017458) Copy
https://github.com/r3fang/SnapATAC
Software package for analyzing scATAC-seq datasets.Used to dissects cellular heterogeneity in unbiased manner and map trajectories of cellular states. Can process data from up to million cells. Incorporates existing tools into comprehensive package for analyzing single cell ATAC-seq dataset.
Proper citation: SnapATAC (RRID:SCR_020981) Copy
https://www.nitrc.org/projects/neurolabels
This resource was created to host descriptions of protocols, definitions and rules for the reliable identification and localization of human brain anatomy and discussions of best practices in brain labeling. Project for manual anatomical labeling of human brain MRI data, and the visual presentation of labeled brain images.
Proper citation: BrainColor: Collaborative Open Labeling Online Resource (RRID:SCR_006377) Copy
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