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https://github.com/atakanekiz/CIPR-Package

Software R package for annotating cell clusters in scRNAseq data.

Proper citation: CIPR-Package (RRID:SCR_027697) 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://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.revvity.com/

American company in the life sciences and diagnostics business that is focused on selling to the pharmaceutical and biotechnology industries, especially in relation to approaches making use of new cell therapy or gene therapy developments.

Proper citation: Revvity Inc. (RRID:SCR_027779) 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://github.com/YingZ-A3D3a/A3D3a_MVP

Software tool as novel graph-based, cooperativity-led Markov chain model to exploit cooperativity of weak signals within cancer molecular network to enhance the signal of true molecular vulnerabilities. Used to identify molecular vulnerabilities from multimodal patient data.

Proper citation: A3D3a MVP (RRID:SCR_027712) Copy   

•   Source: SciCrunch Registry

https://gricad-gitlab.univ-grenoble-alpes.fr/nanobubbles/pcl_detector

Software tool to detect problematic cell lines during text processing.Based on: SciSpacy NER model "en_ner_jnlpba_md" -- DNA, Cell Type, RNA, Protein, Cell Line Cellosaurus (Dump, FEV. 2021) and ICLAC (V10).

Proper citation: PCL_detector (RRID:SCR_027703) 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

https://www.bio-rad.com/fr-fr/sku/12015392-ptc-tempo-deepwell-thermal-cycler?ID=12015392

Conventional PCR instrument built with fixed 96-deepwell reaction block that accommodates reaction volumes of 10 ul to up to 125 µl.

Proper citation: Bio-Rad: PTC Tempo Deepwell Thermal Cycler (RRID:SCR_027704) Copy   

•   Source: SciCrunch Registry

https://www.utsouthwestern.edu/research/core-facilities/histo-pathology/

Core offers research histology and anatomic pathology services and customized pathology services. Facilitates morphologic and histologic assessment of murine transgenic and knockout phenotypes as well as experimental procedure-based models of disease for basic and clinical research. We utilize expertise in gross pathology, routine histology, immunohistochemistry, tissue microarray, spatial transcriptomics, spatial proteomics, laser-capture microdissection, materials science, photomicrography, and image analysis.

Proper citation: University of Texas Southwestern Medical Center Dallas Histo Pathology Core Facility (RRID:SCR_027706) Copy   

•   Source: SciCrunch Registry

https://viceprovost.tufts.edu/flow-cytometry-core

Core offers Flow and Laser Cytometry equipment and services including FACS Analysis and Cell Sorting, to the scientific community.

Proper citation: Tufts University Laser Cytometry Core Facility (RRID:SCR_027709) Copy   

•   Source: SciCrunch Registry