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https://www.brain-score.org/

Platform provides accurate, machine-executable computational models of how the brain gives rise to the mind. Enables researchers to quickly get a sense of the alignment of their model(s) to neural and behavioral measurements, and provides these models to experimentalists to prototype new experiments and make sense of biological data. All code is open-source and community members may choose to make their data or model weights fully public.

Proper citation: Brain Score (RRID:SCR_027769) Copy   

•   Source: SciCrunch Registry

https://www.mskcc.org/research/ski/core-facilities/integrated-genomics-operation-igo

Core provides services and expertise to Center investigators interested in evaluating gene expression, chromosome structure, and nucleotide sequence on a broad scale. Enables basic, clinical, and translational research projects across the Center. Through its production group, the Core enables genomic and transcriptomic analyses and has the expertise to process challenging samples from all origins (tissue, dissociated single cells and cell pellets, paraffin curls, blood, serum, etc.). Bulk DNA/RNA assays operate in highly automated environment, from sample reception to sequencing library preparation.

Proper citation: Memorial Sloan Kettering Cancer Center Integrated Genomics Operation Core Facility (RRID:SCR_027801) Copy   

•   Source: SciCrunch Registry

https://github.com/McGranahanLab/TcellExTRECT

Software R package to calculate T cell fractions from WES data from hg19 or hg38 aligned genomes.

Proper citation: T Cell ExTRECT (RRID:SCR_027742) Copy   

•   Source: SciCrunch Registry

https://github.com/vanallenlab/comut

Software Python library for creating comutation plots to visualize genomic and phenotypic information. Used for visualizing genomic and phenotypic information via comutation plots.

Proper citation: CoMUT (RRID:SCR_027745) Copy   

•   Source: SciCrunch Registry

https://github.com/cancerit/telomerecat

Software R package for estimating average telomere length (TL) for paired end, whole genome sequencing (WGS) sample.Telomere computational analysis tool.

Proper citation: Telomerecat (RRID:SCR_027747) Copy   

•   Source: SciCrunch Registry

http://bionlp.bcgsc.ca/cancermine/

Text-mined and routinely updated database of drivers, oncogenes and tumor suppressors in different types of cancer.

Proper citation: CancerMine (RRID:SCR_027748) Copy   

•   Source: SciCrunch Registry

https://github.com/Zhao-Lab-UW/SAMS-Semi-Automatic-MEA-Spike-sorting-pipeline-

Software MATLAB-based application for spike sorting multi-electrode array (MEA) recordings. Used for efficient, reproducible spike sorting in high-throughput neuronal culture experiments. SAMS performs batched automated spike sorting processes and also allows the users to review and correct any clusters or spike assignments.

Proper citation: Semi-Automated MEA Spike Sorting (SAMS) (RRID:SCR_027843) Copy   

•   Source: SciCrunch Registry

https://github.com/Illumina/canvas

Software tool for calling copy number variants (CNVs) from human DNA sequencing data. It can work either with germline data, or paired tumor/normal samples. Its primary input is aligned reads (in .bam format), and its primary output is a report (in a .vcf file) giving the copy number status of the genome.

Proper citation: Canvas Copy Number Variant Caller (RRID:SCR_027970) Copy   

•   Source: SciCrunch Registry

https://github.com/cortex-lab/phy

Software open-source Python library providing graphical user interface for visualization and manual curation of large-scale electrophysiological data. It is optimized for high-density multielectrode arrays containing hundreds to thousands of recording sites.

Proper citation: Phy (RRID:SCR_027975) Copy   

•   Source: SciCrunch Registry

https://opensourcephysics.github.io/tracker-website/

Software video analysis and modeling tool developed within the Open Source Physics (OSP) Java framework. Allows frame-by-frame tracking of anatomical landmarks and articulated structures from video recordings, enabling the extraction of time-dependent kinematic variables such as displacement, velocity, and acceleration. Tracker is well suited for biomechanical analyses of articulated systems, as it supports joint-based rotations, reference-frame definition, and the export of quantitative motion data for further post-processing.

Proper citation: Tracker (RRID:SCR_027845) Copy   

•   Source: SciCrunch Registry

https://github.com/brain-bican/developing_human_brain_atlas_ontology

Machine-readable framework designed to standardize, organize, and annotate the anatomical structures, developmental stages, and spatial relationships of the human brain during development. It is primarily derived from the Allen Developing Human Brain Atlas (BrainSpan) to provide a structured, hierarchical taxonomy for researchers. Application ontology built by combining ontologised versions of the Allen Institute Developing Human Brain Atlas (DHBA) StructureGraph mapped to Uberon.

Proper citation: Developmental Human Brain Atlas Ontology (DHBA) (RRID:SCR_027940) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/piecewiseSEM/index.html

Software R package for performing Piecewise Structural Equation Modeling, designed to fit complex causal networks by breaking them into smaller, manageable "pieces" (individual regressions) rather than using global covariance estimation. Used to analyze complex, direct/indirect ecological and evolutionary data.

Proper citation: piecewiseSEM (RRID:SCR_027935) Copy   

•   Source: SciCrunch Registry

https://github.com/JeffLuo9/Hep_Ploidy_protocol/

Software hepatocyte ploidy identification pipeline on the stereo-cell platform for accurate liver polyploidy classification via fluorescence staining and deep learning tools.

Proper citation: SCIPI (RRID:SCR_027939) Copy   

•   Source: SciCrunch Registry

https://github.com/schwartzlab-methods/CellNEST

Software tool to decipher patterns of communication. Used to relay-network communication detection that identifies putative ligand–receptor–ligand–receptor communication. Detects T cell homing signals in human lymph nodes, identifies aggressive cancer communication in lung adenocarcinoma and colorectal cancer, and predicts new patterns of communication that may act as relay networks in pancreatic cancer.

Proper citation: CellNEST (RRID:SCR_027883) Copy   

•   Source: SciCrunch Registry

https://github.com/BGI-Qingdao/4D-BioReconX

Software bioinformatic framework for reconstructing 4D spatial transcriptomics atlas and spatiotemporal analyses+.

Proper citation: 4D-BioReconX (RRID:SCR_027919) Copy   

•   Source: SciCrunch Registry

http://pl64.com

Software versatile all-purpose image and graphics editor for Windows, macOS, and Linux (via Wine) that combines raster (bitmap) and vector editing, making it a strong, affordable alternative to Adobe Photoshop, with features like layers, masks, color management (CMYK, Lab, 16-bit), batch processing, and web tools, presented in a comprehensive yet sometimes retro-looking interface . You can edit images or optimize them for the web, but you can also prepare print-ready PDF data.

Proper citation: Photoline (RRID:SCR_027878) Copy   

•   Source: SciCrunch Registry

https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction

Software tool for cell type specific enhancer-gene predictions using ABC model.

Proper citation: ABC-Enhancer-Gene-Prediction (RRID:SCR_027918) Copy   

•   Source: SciCrunch Registry

https://github.com/ay-lab/fithic

Software tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

Proper citation: Fit-Hi-C (RRID:SCR_027917) Copy   

•   Source: SciCrunch Registry

https://camera.niehs.nih.gov/

Interactive database and user interface providing online access to validated alternative methods for U.S. regulatory and other contexts of use. Central hub and unified resource of validated alternative methods that enhances accessibility to validation study reports, data, protocols / SOPs, and information on regulatory guidance.Users can filter searches by alternative method types, defined approaches, Test Method Endpoint, and regulatory guidance.

Proper citation: Collection of Alternative Methods for Regulatory Application (CAMERA) (RRID:SCR_027893) Copy   

•   Source: SciCrunch Registry

https://icv.institutducerveau.org/service/overview-celis-ips/

As part of the cellular engineering and vectorology core facility (ICV), the iPSC core facility (ICV-iPS) proposes the generation and the genetic engineering of human induced pluripotent stem cells to internal research teams, external academic teams, and industrial partners. Services include generation of human iPSc with Sendai virus, full molecular and functional characterization of iPSc clones, genetic engineering of human iPSc with CRISPR/Cas9 system and theoretical and practical learning sessions on human iPSc culture. The core facility provides also access to L2 cell culture box dedicated to human iPSc culture.

Proper citation: Paris Brain Institute iPSC Core Facility (RRID:SCR_027891) Copy   

•   Source: SciCrunch Registry