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https://github.com/chrisgorgo/alleninf

Software package to test hypotheses about relation of patterns found in statistical maps with gene expression measured in postmortem brains. Refines corregistration coordinates provided by the Allen Institute.Used to compare statistical map of brain with gene expression patterns from Allen Human Brain Atlas.

Proper citation: Alleninf (RRID:SCR_023837) Copy   

•   Source: SciCrunch Registry

https://github.com/zhenzonglei/abat

Software stores mutiple MATLAB functions to read, analyze, and visualize various kinds of data from Allen Brain Atlas.

Proper citation: Allen Brain Atlas Tools (RRID:SCR_023855) Copy   

•   Source: SciCrunch Registry

https://abagen.readthedocs.io/en/stable/

Software package provides Python interface for aquiring and analyzing Allen Human Brain Atlas microarray expression data.Includes reproducible workflow for processing microarray expression data for further analysis.Used for the Allen Brain Atlas genetics data.

Proper citation: Abagen (RRID:SCR_023832) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/ABAEnrichment//

Software R package that tests for expression enrichment in specific brain regions at different developmental stages using expression information gathered from multiple regions of the adult and developing human brain, together with ontologically organized structural information about the brain, both provided by the Allen Brain Atlas.Used to test for gene set expression enrichment in adult and developing human brain.

Proper citation: ABAEnrichment (RRID:SCR_023814) Copy   

•   Source: SciCrunch Registry

https://github.com/macarenasa/goi2roimapping

Software Python package utilizes spatial, anatomical, microarray expression data from the Allen Institute for Brain Science. This program maps genes of interest (Goi) by their levels of expression to brain regions (Roi). The identified regions that co-express the input Goi can, in turn, be studied further with many experimental modalities. This program can be customized to map gene expression data and identify significant Roi from similar reference expression data in other contexts outside of neuroscience.

Proper citation: goi2roimapping (RRID:SCR_023820) Copy   

•   Source: SciCrunch Registry

https://github.com/brainglobe/bg-atlasapi

Software lightweight python module to interact with atlases for systems neuroscience. Provides consistent way to process brain atlas data from various sources.

Proper citation: BrainGlobe Atlas API (RRID:SCR_023848) Copy   

•   Source: SciCrunch Registry

http://fair.dei.unipd.it/software/

Software platform for integration of imaging data and Allen Human Brain Atlas mRNA data. MENGA investigates correlation patterns between various imaging modalities and gene expression profiles based on the Allen Brain Atlas in order to create comprehensive, integrated data platform.

Proper citation: Multimodal Environment for Neuroimaging and Genomic Analysis (RRID:SCR_023822) Copy   

•   Source: SciCrunch Registry

https://github.com/brainglobe/brainreg-segment

Software tool for manual segmentation of regions/objects within the brain. Brainreg-segment will only work if the user registers their data with brainreg first. Used for segmentation of 3D shapes in common anatomical space.

Proper citation: Brainreg-segment (RRID:SCR_023853) Copy   

•   Source: SciCrunch Registry

https://github.com/brainglobe/brainreg

Software Python based tool that registers the template brain (e.g. from the Allen Reference Atlas) to the sample image.Automated 3D brain registration with support for multiple species and atlases.

Proper citation: Brainreg (RRID:SCR_023858) Copy   

•   Source: SciCrunch Registry

https://www.ebrains.eu/brain-atlases/analysis/gene-expression-analysis-in-human-brain-atlas-regions/

Software tool for integrating tissue transcriptome and cytoarchitectonic segregation. Combines data from Allen Human Brain Atlas and the EBRAINS Human Brain Atlas, specifically to discover how gene activities and microanatomical architectures contribute to brain function and dysfunction. Both tissue transcriptome and probabilistic brain segregation data allow for integrating genetic expression, brain structure, and function knowledge.

Proper citation: JuGEx (RRID:SCR_023838) Copy   

•   Source: SciCrunch Registry

https://github.com/GuillermoPoblete/PGL

Software R package which links genetics and human brain imaging by using genes associated with disease and calculating normalized mRNA expression average of those genes in each brain region. By uploading lists of genes and brain regions of interest, this package will return csv with the results.

Proper citation: Process Genes List (RRID:SCR_023823) Copy   

•   Source: SciCrunch Registry

https://rdrr.io/cran/WGCNA/man/BrainRegionMarkers.html

Software R package provides matrix of predefined set of marker genes for many regions of the human brain, using data from the Allen Human Brain Atlas.

Proper citation: BrainRegionMarkers (RRID:SCR_023836) Copy   

•   Source: SciCrunch Registry

https://github.com/benfulcher/GCEA_FalsePositives

Software toolbox for gene category enrichment analysis false positives available. Used for analysis of statistical biases in Gene Set Enrichment Analysis applied to transcriptomic atlas data.

Proper citation: GCEA_FalsePositives (RRID:SCR_023835) Copy   

•   Source: SciCrunch Registry

https://github.com/LeonDLotter/ABAnnotate/tree/v0.1.0

Software toolbox for ensemble-based multimodal gene-category enrichment analysis of human neuroimaging data.Performs ensemble-based gene-category enrichment analysis on volumetric human neuroimaging data via brain-wide gene expression patterns derived from Allen Human Brain Atlas. Utilizes nonparametric method using spatial autocorrelation-corrected phenotype null maps for estimation of gene-category null ensembles.

Proper citation: ABAnnotate (RRID:SCR_023833) Copy   

•   Source: SciCrunch Registry