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https://bioconductor.org/packages/CNVMetrics/

Software R package to calculate similarity metrics to facilitate copy number variant comparison among samples and/or methods.

Proper citation: CNVMetrics (RRID:SCR_027263) Copy   

•   Source: SciCrunch Registry

https://wertheim.scripps.ufl.edu/cores-and-technologies/flow-cytometry/

Core provides flow cytometry and cell sorting services.

Proper citation: University of Florida Scripps Institute for Biomedical Innovation and Technology Flow Cytometry Core Facility (RRID:SCR_027278) Copy   

•   Source: SciCrunch Registry

https://www.augusta.edu/cancer/research/shared-resources/biorepository/

Core provides collection, annotation, and storage solutions. This Biorepository is also home to a state-wide resource, the Biorepository Alliance of Georgia for Oncology (BRAG-Onc), which functions to collect samples from 6 participating sites across the State to represent the diversity of cancer patients within the State and to enhance cancer research in Georgia.Tissue specimens are fast-frozen in vapor phase liquid nitrogen to preserve their integrity and stored in large cryofreezers at -170 to -190°C. Blood is routinely separated into serum or plasma and buffy coats prior to freezing. Blood derivatives are stored at -70 to -80°C. The freezers are monitored constantly and are connected to an alarm system to ensure that the low temperatures are maintained.

Proper citation: Augusta University Georgia Cancer Center Biorepository Core Facility (RRID:SCR_027271) Copy   

•   Source: SciCrunch Registry

https://github.com/Kataoka-K-Lab/Celline

Software Python pipeline for one-step retrieval and integrative analysis of public single-cell RNA sequencing data.

Proper citation: Celline (RRID:SCR_027273) Copy   

•   Source: SciCrunch Registry

https://www.crukscotlandinstitute.ac.uk/advanced-technologies/molecular-technology.html

Core provides Next Generation Sequencing (NGS) services and Single Cell services predominantly focussing on single cell RNAseq. Processes samples for variety of cancer associated projects, in both mouse and human derived materials. Offers full end-to-end service, from initial study design and planning, through sample QC, full library preparation, sequencing and data return. Offers range of standard molecular tests covering, plasmid purifications, Sanger sequencing and mycoplasma screening.

Proper citation: Cancer Research UK Scotland Institute Molecular Technology Service Core Facility (RRID:SCR_027368) Copy   

•   Source: SciCrunch Registry

https://github.com/adeschen/enrichViewNet

Software package for visualization of functional enrichment results as network graphs.

Proper citation: enrichViewNet (RRID:SCR_027256) Copy   

•   Source: SciCrunch Registry

https://research.weill.cornell.edu/core-facilities/human-therapeutic-organoid-core

Facility serves as central facility for human organoid technology to accelerate organoid-based scientific discovery. Provides human pluripotent stem cell (hPSC) derived as well as tissue derived cells and organoids.

Proper citation: Weill Cornell Medicine Human Therapeutic Organoid Core Facility (RRID:SCR_027251) Copy   

•   Source: SciCrunch Registry

https://cloud.sylabs.io/library/jsaraiva/repo/hvrlocator

Software application to identify spanning hypervariable region(s) from amplicon sequencing variants or SRA public runs (SRR). Aligns query sequences to reference E. coli full-length 16S rRNA gene and identifies spanning region through alignment. Used for identifying hypervariable regions in 16S rRNA big datasets.

Proper citation: HVRLocator (RRID:SCR_027407) Copy   

•   Source: SciCrunch Registry

https://github.com/songlabcodes/MSC

Software R package for multi-scale clustering to perform single-cell transcriptome clustering.

Proper citation: Multi Scale Clustering (RRID:SCR_027342) Copy   

•   Source: SciCrunch Registry

https://www.ucl.ac.uk/lifesciences-faculty/laboratory-molecular-cell-biology/research/platforms-and-facilities/electron-microscopy

Electron microscopy facility specialising in cell biological electron microscopy for basic and medical research applications.

Proper citation: University College London LMCB Electron Microscopy Core Facility (RRID:SCR_027340) Copy   

•   Source: SciCrunch Registry

https://github.com/wenmm/EssSubgraph/tree/main

A model algorithm that integrates omics data and network data to predict essential genes.

Proper citation: EssSubgraph (RRID:SCR_027354) Copy   

•   Source: SciCrunch Registry

https://github.com/rnajena/dynamont

Software segmentation/resquiggling tool for ONT signals. Dynamic programming approach to segment ONT signals.

Proper citation: Dynamont (RRID:SCR_027357) Copy   

•   Source: SciCrunch Registry

https://github.com/Baohua-Chen/GFFx

Software Rust-Based suite of utilities for ultra-fast genomic feature extraction. Used for ultra-fast and scalable genome annotation access. Can be used both as a command-line tool and as a Rust library.

Proper citation: GFFx (RRID:SCR_027445) Copy   

•   Source: SciCrunch Registry

http://www.drive5.com

Software application that provides search and clustering functionality, typically used with amplicon sequence data. Used to assign sequences to clusters.

Proper citation: USEARCH (RRID:SCR_027438) Copy   

•   Source: SciCrunch Registry

http://confocal.uconn.edu

Facility provides training and access to advanced light microscopy systems at an hourly rate. In addition, we are available to consult with and support users at every stage of a project including: experimental design, sample preparation, image acquisition, analysis, and data preparation.

Proper citation: University of Connecticut Advanced Light Microscopy Core Facility (RRID:SCR_027547) Copy   

•   Source: SciCrunch Registry

https://github.com/jzhang-dev/FEDRANN

Software scalable pipeline for overlap detection based on large-scale sequencing data. It is based on three steps: feature extraction, dimenality reduction, and approximate k-nearest neighbor search. Used for effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors.

Proper citation: Fedrann (RRID:SCR_027416) Copy   

•   Source: SciCrunch Registry

https://github.com/kermitt2/grobid

Software tool for extracting information from scholarly documents.

Proper citation: Grobid (RRID:SCR_027539) Copy   

•   Source: SciCrunch Registry

https://github.com/hejDMC/napari-dmc-brainmap

Software napari plugin for flexible mapping of various features (cell bodies, axonal densities, injections sites, optical fibers, Neuropixels probes) to standardized reference spaces included in BrainGlobe. Used for anatomical mapping.

Proper citation: DMC-BrainMap (RRID:SCR_027433) Copy   

•   Source: SciCrunch Registry

https://github.com/hejDMC/dmc-fluoimager

Software Python project for whole slide image acquisition using a fluorescence microscope.

Proper citation: DMC-FluoImager (RRID:SCR_027435) Copy   

•   Source: SciCrunch Registry

https://github.com/jmschrei/memesuite-lite

Software application as lightweight reimplementation of some of the algorithms in the MEME suite in Python.

Proper citation: memesuite-lite (RRID:SCR_027429) Copy   

•   Source: SciCrunch Registry