Tools   Select Another Resource Report Type

https://stardist.net/

Software application for object detection with Star-convex Shapes. Used for phase-contrast cell images.

Proper citation: StarDist (RRID:SCR_027715) Copy   

•   Source: SciCrunch Registry

https://fivepseq-explorer.serve.scilifelab.se/app/fivepseq-explorer

Web-based platform for interactive exploration of ribosome dynamics derived from 5′P mRNA degradome sequencing (5PSeq) data. Focused on changes in ribosome dynamics associated to mRNA decay that in some cases can be obscured in conventional ribosome profiling data.

Proper citation: 5PSeq Explorer (RRID:SCR_027718) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/bbglab/oncodriveclustl/src/master

Software application to detect significant clustering signals across genomic regions. Sequence-based clustering method to identify cancer drivers.

Proper citation: OncodriveCLUSTL (RRID:SCR_027730) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/bbglab/oncodrivefml/src/master

Software tool that estimates accumulated functional impact bias of somatic mutations in any genomic region of interest based on local simulation of the mutational process affecting it.

Proper citation: OncodriveFML (RRID:SCR_027731) Copy   

•   Source: SciCrunch Registry

https://github.com/bbglab/intogen-plus

Software tool for automatic and comprehensive knowledge extraction based on mutational data from sequenced tumor samples from patients. Summarizes somatic mutations, genes and pathways involved in tumorigenesis.

Proper citation: IntOGen (RRID:SCR_027727) Copy   

•   Source: SciCrunch Registry

https://github.com/eyzhao/hrdetect-pipeline

Software tool for detection and analysis of homologous recombination events.

Proper citation: HRDetect (RRID:SCR_027726) Copy   

•   Source: SciCrunch Registry

https://github.com/vanallenlab/MutPanningV2

Software tool designed to detect rare cancer driver genes from aggregated whole-exome sequencing data.

Proper citation: MutPanningV2 (RRID:SCR_027729) Copy   

•   Source: SciCrunch Registry

https://github.com/sheenamt/msings

Software tool for detecting microsatellite instability by next-generation sequencing.

Proper citation: mSings (RRID:SCR_027728) Copy   

•   Source: SciCrunch Registry

https://github.com/noahbenson/neuropythy

Software neuroscience library for Python, intended to complement the existing nibabel library. Can automatic download data and interpret them into Python data structures.

Proper citation: neuropythy (RRID:SCR_027787) Copy   

•   Source: SciCrunch Registry

https://icahn.mssm.edu/research/resources/deans-cores/flow-cytometry

Situated within the Icahn School of Medicine at Mount Sinai, our CoRE provides all members of the Mount Sinai Health System community with the instrumentation, expertise, and education required to incorporate flow cytometry and cell sorting into any research project.

Proper citation: Icahn School of Medicine at Mount Sinai Flow Cytometry CoRE Core Facility (RRID:SCR_027701) Copy   

•   Source: SciCrunch Registry

https://ccg.uni-koeln.de/

Represents central facility and does not operate for profit, engaging in academic research collaborations and service provision on collaborative basis. Provides infrastructure for all kinds of sequencing, gene mapping and whole genome association studies in complex diseases as well as the validation of copy number variations.

Proper citation: University of Cologne Center for Genomics (CCG) Core Facility (RRID:SCR_027822) Copy   

•   Source: SciCrunch Registry

https://www.mskcc.org/research/ski/core-facilities/biostatistics

Core provides expertise on study design and statistical analysis. Devoted to developing and understanding ways to derive scientific inferences from quantitative data and to developing methods for achieving this aim. The staff are highly trained in this field and experienced in all of the specialized areas of statistical techniques including clinical trials methodology, survival analysis, epidemiologic methods, analysis of genomics data, statistical genetics, methods for diagnostic medicine, health services research, survivorship, evidence-based medicine and psychometric methods.

Proper citation: Memorial Sloan Kettering Cancer Center Biostatistics Core Facility (RRID:SCR_027821) Copy   

•   Source: SciCrunch Registry

https://www.nbdc-datahub.org

Data platform providing centralized and secure access to rich, longitudinal brain, behavioral, and genomic data from both the Adolescent Brain Cognitive Development (ABCD) and the HEALthy Brain and Child Development (HBCD) Studies. By bringing together data from both studies, the NBDC Data Hub facilitates integrative research on early life and adolescent development, helping researchers explore developmental trajectories across the lifespan.

Proper citation: NIH Brain Development Cohorts (NBDC) Data Hub (RRID:SCR_027710) Copy   

•   Source: SciCrunch Registry

https://liana-py.readthedocs.io/en/latest/

Software framework that adapts and extends existing methods and knowledge to study cell-cell communication in single-cell, spatially-resolved, and multi-modal omics data. All-in-one framework for cell-cell communication inference.

Proper citation: LIANA+ (RRID:SCR_027830) Copy   

•   Source: SciCrunch Registry

https://github.com/HarmonizedMRI/Functional

Software application for vendor-neutral, open-source acquisition and reconstruction protocols for fully harmonized multi-site functional MRI studies.

Proper citation: Functional (RRID:SCR_027832) Copy   

•   Source: SciCrunch Registry

https://cam.msu.edu/

Core provides instruction and access to scanning electron microscopes, transmission electron microscopes, laser capture microscopes, and confocal laser scanning microscopes. CAM staff members help with microscopes and microscopy analysis.

Proper citation: Michigan State University Center for Advanced Microscopy Core Facility (RRID:SCR_027702) Copy   

•   Source: SciCrunch Registry

http://tucf-genomics.tufts.edu/

Core provides protein sequencing services including Next-Generation DNA Sequencing, Peptide Synthesis, Protein Sequencing, and Mass Spectrometry. Provides expert technical and analytical support.

Proper citation: Tufts University Genomics Core Facility (RRID:SCR_027708) Copy   

•   Source: SciCrunch Registry

https://www.digitalpsych.org/mindlamp1.html

Core collects data to capture and consider the real-time lived experiences of patients. Uses open-source digital platform and mobile app for neuropsychiatric research and clinical care, to monitor, support, and improve brain health by collecting real-time data (like location, activity, heart rate via sensors), conducting digital assessments (surveys, cognitive tests), and delivering interventions (meditation, journaling, psychoeducation) to patients and clinicians. It helps study behavioral patterns, track symptoms, and personalize mental health treatment through features organized around Learn, Assess, Manage, and Prevent.

Proper citation: BIDMC Division of Digital Psychiatry LAMP platform Core Facility (RRID:SCR_027767) Copy   

•   Source: SciCrunch Registry

https://anc.plus.ac.at/

Platform for sustainable research data management in cognitive neuroscience. Secure data storage and integrated tools to support maintenance, reuse, and FAIR-aligned management of neurocognitive research data. Data remains curated, documented, and accessible for the long term, supporting reproducibility and future discovery.

Proper citation: Austrian NeuroCloud (RRID:SCR_027771) Copy   

•   Source: SciCrunch Registry

https://www.uio.no/english/services/it/research/sensitive-data/

Platform to collect, store and analyze sensitive research data in secure environment. It comprises secure project area and integrated solution for collecting sensitive data (Nettskjema), accessible by anywhere in the world.

Proper citation: University of Oslo Services for sensitive data (TSD) (RRID:SCR_027773) Copy   

•   Source: SciCrunch Registry