Tools   Select Another Resource Report Type

https://github.com/MANO-B/U3-Nomogram

Software application for C-CAT CALICO database. Used for Germline-focUsed analysis of tUmoUr-detected variants with Nomogram for C-CAT CALICO database.

Proper citation: U3-Nomogram (RRID:SCR_027696) 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://cran.r-project.org/web/packages/sandwich/index.html

Object-oriented software for model-robust covariance matrix estimators. Starting out from the basic robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC) covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC) covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators); clustered covariances (one-way and multi-way); panel and panel-corrected covariances; outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted to other classes through S3 methods.

Proper citation: sandwich (RRID:SCR_027691) Copy   

•   Source: SciCrunch Registry

https://github.com/ncc-gap/GCATWorkflow

Software cancer genome and RNA sequencing data analysis pipeline that detects genomic variants and transcriptomic changes.

Proper citation: GCAT Workflow (RRID:SCR_027692) 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://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://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://github.com/instadeepai/instanovo

Source code for training and inference of InstaNovo and InstaNovo+. InstaNovo is a transformer neural network with the ability to translate fragment ion peaks into the sequence of amino acids that make up the studied peptide(s).

Proper citation: InstaNovo (RRID:SCR_027758) 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

https://cran.r-project.org/package=AER

Software R package contains functions, data sets, examples, demos, and vignettes for the book Christian Kleiber and Achim Zeileis (2008), Applied Econometrics with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2.

Proper citation: AER: Applied Econometrics with R (RRID:SCR_027778) Copy   

•   Source: SciCrunch Registry

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://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