Tools   Select Another Resource Report Type

https://github.com/ddarriba/modeltest

Software tool for selecting the best-fit model of evolution for DNA and protein alignments. Used for selection of DNA and Protein evolutionary models.

Proper citation: modeltest (RRID:SCR_026633) Copy   

•   Source: SciCrunch Registry

https://github.com/Neural-Systems-at-UIO/CreateZoom/tree/main

Backend application to process high-resolution histology images to DeepZoomImage format, made of smaller tiles, for use in the QUINT Workflow.

Proper citation: CreateZoom (RRID:SCR_026625) Copy   

•   Source: SciCrunch Registry

https://github.com/aertslab/PUMATAC

Software pipeline for universal mapping of ATAC-seq.

Proper citation: PUMATAC (RRID:SCR_026624) Copy   

•   Source: SciCrunch Registry

https://www.labservis.com/en/cobas_8000_analyzer_series_e602

Immunochemistry analyzer as mid-volume throughput immunochemistry module that performs broad range of heterogeneous immunoassay tests using ElectroChemiLuminescence (ECL) technology. Offers Heterogeneous immunoassays, Throughput of up to 170 tests/hour, 25 reagent positions, Reagent cassette loading/unloading during standby, Carryover-free disposable tips, Clot and air bubble detection.

Proper citation: Roche: cobas e 602 analytical unit (RRID:SCR_026640) Copy   

•   Source: SciCrunch Registry

https://biobox.io/

Platform to help scientists organize all biological knowledge into singular, unified resource that is searchable, accessible and capable of answering the most difficult questions in science. Used for bioinformatics analysis.

Proper citation: BioBox (RRID:SCR_026642) Copy   

•   Source: SciCrunch Registry

https://github.com/buenrostrolab/scPrinter

Softwre framework for multi-scale footprinting analysis of single-cell ATAC-seq data. Designed to identify and visualize regulatory elements that drive cell-type-specific gene expression programs through footprinting. Uses deep learning model to predict activity of transcription factors from single-cell ATAC-seq data. Provides suite of visualization tools to explore calculated multi-scale footprints.

Proper citation: scPrinter (RRID:SCR_026644) Copy   

•   Source: SciCrunch Registry

https://rnacomposer.cs.put.poznan.pl/

Web application as fully automated RNA structure modeling server. Used for RNA tertiary structure prediction.

Proper citation: RNAcomposer (RRID:SCR_026636) Copy   

•   Source: SciCrunch Registry

https://www.corelaboratory.abbott/us/en/offerings/brands/architect/architect-i2000SR.html

Analyzer offers maximum throughput of up to 200 tests per hour. Featuring load-up capacity of 135 samples with 35 priority and 100 routine areas. Has 25 refrigerated reagent positions. Designed for efficient and accurate analysis of various biological samples, including serum, plasma, and other bodily fluids.

Proper citation: Abbott: ARCHITECT i2000SR immunoassay analyzer (RRID:SCR_026638) Copy   

•   Source: SciCrunch Registry

https://hex.loria.fr/

Web FFT-based protein docking server. First Fourier transform (FFT)-based protein docking server to be powered by graphics processors.Interactive protein docking and molecular superposition program. Hex understands protein and DNA structures in PDB format, and it can also read small-molecule SDF files.Hex will run on most Windows-XP, Linux and Mac OS X PCs.

Proper citation: Hex (RRID:SCR_026637) Copy   

•   Source: SciCrunch Registry

https://www.agilent.com/en/product/cell-analysis/real-time-cell-metabolic-analysis/xf-analyzers/seahorse-xf-pro-analyzer-1980223?Product_Interest_Source=Marketing%20Campaign&source=Marketing%20Campaign&Lead_Campaign_Source=7015Y000003dRP4QAM&Campaign_Source=7015Y000003dRP4QAM&gad_source=1&gclid=Cj0KCQjwna6_BhCbARIsALId2Z3FeXTy8xavZm2HteJhWfj_gvyV9m490sjaBA3tyImLsLRcYPCBxDoaAi95EALw_wcB&gclsrc=aw.ds

Agilent Seahorse XF Pro analyzer measures and reports the oxygen consumption rate (OCR), proton efflux rate (PER) or extracellular acidification rate (ECAR), as well as ATP production rates of live cells in a 96-well format. This analyzer features excellent OCR precision at low rates, verified performance, optimized temperature control, and is automation enabled. The XF Pro analyzer is also equipped with advanced software, standardized workflows, and advanced data analytics available in the Agilent Seahorse Analytics software. These features greatly simplify the entire XF assay experience, from assay design to data QC and interpretation.

Proper citation: Agilent: Seahorse XF Pro Analyzer (RRID:SCR_026694) Copy   

•   Source: SciCrunch Registry

https://medresearch.umich.edu/office-research/about-office-research/biomedical-research-core-facilities/vector-core

Vector Core produces gene transfer vectors that facilitate transfer of specific genes into either normal or aberrant cells. Provides intellectual and technical advice to researchers regarding the optimal use of these systems.

Proper citation: University of Michigan Medical School BRCF Vector Core Facility (RRID:SCR_026696) Copy   

•   Source: SciCrunch Registry

https://github.com/broadinstitute/ssGSEA2.0

Software application as updated version of original ssGSEA R-implementation. Depending on the input dataset and chosen database (gene sets or PTM signatures), the software performs either ssGSEA or PTM-SEA, respectively.

Proper citation: ssGSEA 2.0 (RRID:SCR_026610) Copy   

•   Source: SciCrunch Registry

https://www.mdanderson.org/research/research-resources/core-facilities/advanced-microscopy-core.html

Core provides microscopy services to departments at MD Anderson in high resolution and multispectral fluorescence microscopy for users from divisions including Basic Research, Cancer Medicine, Diagnostic Imaging, Surgery, Internal Medicine Pediatrics and Radiation Oncology, among others. Offers microscopy resources and expertise in fluorescence imaging to spatially and dynamically assess cells, tissues and their requisite contents across scales.

Proper citation: University of Texas MD Anderson Cancer Center Advanced Microscopy Core Facility (RRID:SCR_026611) Copy   

•   Source: SciCrunch Registry

https://endomap.hms.harvard.edu/

Structural interactome viewer. Interactive database of endosomal protein-protein interactions identified by cross-linking mass spectrometry and modeled by AlphaFold multimer. Structural protein interactome of human early endosomes.

Proper citation: EndoMap (RRID:SCR_026690) Copy   

•   Source: SciCrunch Registry

https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2

Software tool to call somatic short mutations via local assembly of haplotypes. Somatic variant caller that uses local assembly and realignment to detect SNVs and indels.

Proper citation: Mutect2 (RRID:SCR_026692) Copy   

•   Source: SciCrunch Registry

https://www.liverpool.ac.uk/research/facilities/centre-for-preclinical-imaging/

Provides access to imaging systems. Offers researchers technologies for multi-modality, non-invasive approaches to imaging on small, live animals, or tissues and organs extracted from animals . Our equipment can be used for pre-clinical models and non-biological samples.

Proper citation: University of Liverpool Centre for Preclinical Imaging Core Facility (RRID:SCR_026605) Copy   

•   Source: SciCrunch Registry

https://www.liverpool.ac.uk/research/facilities/histology/

Facility offers preparation of samples from fresh or fixed tissue through to scanned images. Provides training to prepare and use equipment to embed, section and hand stain tissues as required. Offers three different types of wax for embedding and sectioning as required. Fully equipped for methyl methacrylate and glycol methacrylate embedding and sectioning (including larger samples), freeze microtomy and high throughput slide imaging using our Zeiss Axioscan Z1.

Proper citation: University of Liverpool Shared Research Histology Core Facility (RRID:SCR_026606) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/statannotations/

Software Python package to optionally compute statistical test and add statistical annotations on plots generated with seaborn. Used to add statistical significance or custom annotations on seaborn plots.

Proper citation: statannotations (RRID:SCR_026623) Copy   

•   Source: SciCrunch Registry

https://github.com/kaizhang/SnapATAC2

Software Python/Rust package for single-cell epigenomics analysis.

Proper citation: SnapATAC2 (RRID:SCR_026622) Copy   

•   Source: SciCrunch Registry

https://obc.bio.uci.edu/

Shared resource facility to provide researchers access to resources, including state of the art instrumentation and technical support, to conduct biomedical research. Provides access to light microscopes (confocal, mesoscale lightsheet, and Super Resolution), as well as software for 3D and 4D analysis.

Proper citation: University of California at Irvine Optical Biology Core Facility (RRID:SCR_026614) Copy   

•   Source: SciCrunch Registry