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http://fcon_1000.projects.nitrc.org/indi/pro/nki.html
A phenotypically rich neuroimaging sample, consisting of data obtained from individuals between the ages of 4 and 85 years-old. All individuals included in the sample undergo semi-structured diagnostic psychiatric interviews, and complete a battery of psychiatric, cognitive and behavioral assessments in order to provide comprehensive phenotypic information for the purpose of exploring brain / behavior relationships.
Proper citation: NKI/Rockland Sample (RRID:SCR_009435) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MSM
Software tool for registering cortical surfaces. Capable of driving alignment using wide variety of descriptors of brain architecture, function and connectivity.
Proper citation: Multimodal Surface Matching (RRID:SCR_024929) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST
Software model based segmentation and registration tool. Used for segmentation of sub-cortical structures. Introduces basic segmentation and vertex analysis for detecting group differences.
Proper citation: FMRIB’s Integrated Registration and Segmentation Tool (RRID:SCR_024921) Copy
https://github.com/bmvdgeijn/WASP/
Software allele-specific pipeline for unbiased read mapping and molecular QTL discovery. Allele-specific software for robust molecular quantitative trait locus discovery.
Proper citation: WASP (RRID:SCR_025497) Copy
http://casestudies.brain-map.org/celltax
Cellular Taxonomy of Mouse Visual Cortex by analyzing gene expression patterns at single cell level. Construction of cellular taxonomy of one cortical region, primary visual cortex, in adult mice done on basis of single cell RNA sequencing.
Proper citation: CellTax vignette (RRID:SCR_017000) Copy
https://github.com/SchapiroLabor/histoCAT
Software package to visualize and analyse multiplexed image cytometry data interactively.
Proper citation: histoCAT (RRID:SCR_026499) Copy
https://github.com/calico/borzoi
Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences.
Proper citation: Borzoi (RRID:SCR_026619) Copy
BRAIN Initiative data archive for multi-modal neurophysiological and behavioral data, supporting the Brain Behavior Quantification and Synchronization (BBQS) Program. Accessible and versatile data archive for storage, processing, and curation of multimodal neurophysiological and behavioral datasets. EMBER extends established BRAIN Initiative data infrastructure, provides new data harmonization and synchronization capabilities, and supports scalable integrations for data coordination and AI driven batch processing to enable the goals of the BBQS program.
Proper citation: Ecosystem for Multi-modal Brain-behavior Experimentation and Research (RRID:SCR_026700) Copy
https://brain-specimenportal.org/unified_resource_browser?resource_type=donor
Neuroanatomy-anchored Information Management Platform for collaborative BICAN data generation developed by UTHealth Houston. Serves as metadata tracking engine to support generation, management, and sharing of brain research data. Integrates data production pipelines across brain banks, laboratories, sequencing centers, and data archives. Platform enables integrative and collaborative, consortium-scale FAIR data generation within the BICAN project. Platform is designed to manage complex dataset, including tissue samples and sequencing data, through Specimen Portal and Sequence Library Portal. Portals provide multiple types of data interfaces through dashboards, APIs, faceted queries, and batch data ingestion and exporting.
Proper citation: NIMP Analytics (RRID:SCR_028218) Copy
https://github.com/GabrielHoffman/dreamlet
Software R package enables differential expression analysis on multi-sample single cell datasets using linear (mixed) models with precision weights.
Proper citation: dreamlet (RRID:SCR_028168) Copy
https://github.com/meganhuibregtse/peri-code
Software R code to apply Stages of Reproductive Aging Workshop + 10 stages to prospectively collected vaginal bleeding data among a cohort of Black women aged 40–55 years. Used to apply STRAW+10 stages to prospectively tracked menstrual bleeding data in a longitudinal cohort study of perimenopausal women.
Proper citation: PERI: Prospective Evaluation of Reproductive aging Indicators (RRID:SCR_028698) Copy
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