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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

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/janclemenslab/glm_utils

Software tools for fitting Generalized Linear Models (GLMs) with time dependence (a.k.a. filters).

Proper citation: GLM utilities (RRID:SCR_027862) Copy   

•   Source: SciCrunch Registry

https://docs.gspread.org/en/latest/

Software python library for working with Google Sheets allowing users to open spreadsheet by title, key or URL. It also allows to read, write, and format cell ranges and more.

Proper citation: gspread (RRID:SCR_027866) Copy   

•   Source: SciCrunch Registry

https://mic.massgeneralbrigham.org

Core facility that provides microscopy training, imaging solutions, image processing and analysis services, and consultation. Offers imaging techniques and expertise, including spinning disc confocal microscopy, two-photon confocal microscopy, super resolution microscopy, total internal reflection microscopy, wide field microscopy, fluorescence spectroscopy, photo-manipulation techniques (e.g. FRAP, photoablation, optogenetics, and optical tweezers) and live cell imaging.

Proper citation: Massachusetts General Hospital Brigham Center of Excellence for Molecular Imaging Core Facility (RRID:SCR_027865) Copy   

•   Source: SciCrunch Registry

https://github.com/NOW-Lab/STICR

Code to conduct combinatorial barcoding. scRNA-seq-compatible tracer for identifying clonal relationships.

Proper citation: STICR (RRID:SCR_027856) Copy   

•   Source: SciCrunch Registry

https://github.com/blaserlab/blaseRtools/tree/v0.0.0.9202

Software R tools for Blaser Lab Data Analysis. Package includes commonly used functions for R analysis in the Blaser Lab.

Proper citation: blaseRtools (RRID:SCR_027871) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/sivic/

Software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies.

Proper citation: Spectroscopic Imaging, VIsualization, and Computing (SIVIC) (RRID:SCR_027875) Copy   

•   Source: SciCrunch Registry

https://www.siemens-healthineers.com/laboratory-diagnostics/clinical-chemistry-and-immunoassay-systems/atellica-solution-analyzers#assay-menu-area

Mid-volume, automated immunoassay system used in clinical labs to perform a wide range of tests for diagnosing and monitoring diseases, detecting infections, checking hormone levels, and assessing cardiac health, by analyzing biological samples like blood for specific proteins, hormones, and other markers with high reliability and efficiency, often integrated into the larger, flexible Atellica Solution for automated workflows.

Proper citation: Siemens: Atellica IM 1300 Analyzer (RRID:SCR_027876) 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://bio.tools/dupradar

Software R package for assessment of PCR artifacts in RNA-Seq data. Used for duplication rate quality control for RNA-Seq datasets.

Proper citation: dupRadar (RRID:SCR_027976) 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://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/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

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://github.com/mzlab-research/SMIntegration

Software open-source platform for integrated analysis of spatial transcriptomics and metabolomics data. It integrates spatial pattern recognition, differential comparison, network construction, and functional annotation into a unified workflow. Enables to explore gene-metabolite co-regulation mechanisms through an intuitive web interface, revealing spatial heterogeneity in tissue development and disease progression.

Proper citation: SMIntegration (RRID:SCR_027925) Copy   

•   Source: SciCrunch Registry

https://reeflifesurvey.com/

Web interactive digital tool for tracking the health of vital reef ecosystems all around the world. Reef Life Survey program uses scientists and citizen scuba divers to survey fishes on coral and rock reefs throughout the world. Marine life monitoring programm.

Proper citation: Reef Life Survey (RRID:SCR_027928) Copy   

•   Source: SciCrunch Registry