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https://github.com/kstreet13/slingshot

Software R package for identifying and characterizing continuous developmental trajectories in single cell data. Cell lineage and pseudotime inference for single-cell transcriptomics.

Proper citation: Slingshot (RRID:SCR_017012) Copy   

•   Source: SciCrunch Registry

https://community.brain-map.org/t/allen-human-reference-atlas-3d-2020-new/405

Parcellation of adult human brain in 3D, labeling every voxel with brain structure spanning 141 structures. These parcellations were drawn and adapted from prior 2D version of adult human brain atlas.

Proper citation: Allen Human Reference Atlas, 3D, 2020 (RRID:SCR_017764) Copy   

•   Source: SciCrunch Registry

https://openwetware.org/wiki/HughesLab:JTK_Cycle

Software R package for Detecting Rhythmic Components in Genome-Scale Data Sets. Non-parametric algorithm to identify rhythmic components in large datasets. Identifies and characterizes cycling variables in large datasets.

Proper citation: JTK_CYCLE (RRID:SCR_017962) Copy   

•   Source: SciCrunch Registry

https://portal.brain-map.org/atlases-and-data/bkp/mapmycells

MapMyCells maps single cell and spatial transcriptomics data sets to massive, high-quality, and high-resolution cell type taxonomies. It enables speeding up the creation of brain reference atlases by facilitating the integration of datasets from the scientific community with a shared reference. MapMyCells is part of the growing Brain Knowledge Platform. Its key advantage is scale: researchers can provide up to 327 million cell-gene pairs from their own data, a huge leap forward for working with whole-brain datasets. Allen Institute and its collaborators continue to add new reference taxonomies and algorithms to MapMyCells.

Proper citation: MapMyCells (RRID:SCR_024672) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://cells.ucsc.edu/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.brainimagelibrary.org

Repository for confocal microscopy brain imaging data. Data archives that have been established by BRAIN Initiative Data Sharing. National public resource enabling researchers to deposit, analyze, mine, share and interact with large brain image datasets. Operated as partnership between Biomedical Applications Group at Pittsburgh Supercomputing Center, Center for Biological Imaging at University of Pittsburgh and Molecular Biosensor and Imaging Center at Carnegie Mellon University. Provides persistent centralized repository for brain microscopy data.

Proper citation: Brain Image Library (RRID:SCR_017272) Copy   

•   Source: SciCrunch Registry

https://bossdb.org/

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   

•   Source: SciCrunch Registry

https://umgear.org/

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   

•   Source: SciCrunch Registry

https://github.com/PriceLab/TReNA

Methods for reconstructing transcriptional regulatory networks.

Proper citation: TReNA (RRID:SCR_017458) Copy   

•   Source: SciCrunch Registry

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: Pulse Pal (RRID:SCR_017203) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/DeNardoLab/BehaviorDEPOT

Software tool for automated behavioral detection based on markerless pose tracking. Behavioral analysis tool to first compile and clean point-tracking output from DeepLabCut, and then classify behavioral epochs using custom behavior classifiers. Used to detect frame by frame behavior from video time series and can analyze results of common experimental assays, including fear conditioning, decision-making in T-maze, open field, elevated plus maze, and novel object exploration. Calculates kinematic and postural statistics from keypoint tracking data from pose estimation software outputs.

Proper citation: BehaviorDEPOT (RRID:SCR_023602) Copy   

•   Source: SciCrunch Registry

https://github.com/TADA-A/TADA-A/tree/master

Software statistical framework for mapping risk genes from de novo mutations in whole genome sequencing studies.

Proper citation: TADA-A (RRID:SCR_024538) Copy   

•   Source: SciCrunch Registry

https://kimlab.io/brain-map/epDevAtlas/

Suite of open access resources including 3D atlases of early postnatally developing mouse brain and mapped cell type density growth charts, which can be used as standalone resources or to implement data integration. Web platform can be utilized to analyze and visualize the spatiotemporal growth of GABAergic, microglial, and cortical layer-specific cell type densities in 3D. Morphologically averaged symmetric template brains serve as the basis reference space and coordinate system with an isotropic resolution of 20 μm (XYZ in coronal plane). Average transformations were conducted at 20 μm voxel resolution by interpolating high resolution serial two photon tomography images from primarily Vip-IRES-Cre;Ai14 mice at postnatal (P) ages P4, P6, P8, P10, P12, and P14. For all ages, anatomical labels from the P56 Allen Mouse Brain Common Coordinate Framework (Allen CCFv3) were iteratively down registered to each early postnatal time point in a non-linear manner, aided by manual parcellations of landmarks in 3D, consistent with the Allen Mouse Reference Atlas Ontology.

Proper citation: Early Postnatal Developmental Mouse Brain Atlas (RRID:SCR_024725) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/XTRACT

Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain.

Proper citation: XTRACT (RRID:SCR_024933) Copy   

•   Source: SciCrunch Registry