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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://github.com/data61/gossamer/blob/master/docs/xenome.md
Software tool to distinguish host and graft reads from next generation sequencing assays of xenograft samples. Performs classification of xenograft-derived sequence read data.
Proper citation: Xenome (RRID:SCR_026266) Copy
https://www.tomovision.com/products/sliceomatic.html
Medical image analysis software to measure, segment and analyze multi-slice scanner data.
Proper citation: TomoVision sliceOmatic (RRID:SCR_026268) Copy
Genomics core facility with goal to use instrumentation and innovative technical expertise in order to provide investigators with genomic data from comprehensive range of genomic services in timely manner. Services include Next-Generation Sequencing, Sanger Sequencing Single Cell Sequencing, Microarray Services, Fluorescent Fragment Length Analysis, nanoString nCounter Analysis, Bionano Optical Genome Mapping, Spatial Transcriptomics, Nanopore Sequencing.
Proper citation: University of Texas MD Anderson Advanced Technology Genomics Core Facility (RRID:SCR_026261) Copy
https://david-barnett.github.io/microViz/
Software R package for microbiome data visualization and statistics. Docker image available.
Proper citation: microViz (RRID:SCR_026510) Copy
https://www.researchgate.net/publication/265600087_Chronos-Fit_revised_Version_106
Software tool for analysis of biological rhythms, particularly circadian rhythms, using curve fitting methods to model time-series data and determine key parameters such as period, amplitude, and phase.
Proper citation: Chronos-Fit software (RRID:SCR_026472) Copy
https://www.polebio.lrsv.ups-tlse.fr/WallProtDB/
Database resource for plant cell wall proteomics. Aims at collecting cell wall proteomic experimental data. For each experiment, a scheme summarizing the strategy used for protein isolation and identification is provided.
Proper citation: WallProtDB (RRID:SCR_026506) Copy
https://CRAN.R-project.org/package=mice
Software package implements method to deal with missing data. The package creates multiple imputations (replacement values) for multivariate missing data.Various diagnostic plots are available to inspect the quality of the imputations.
Proper citation: mice (RRID:SCR_026363) Copy
https://autodocksuite.scripps.edu/adt/
Software graphical user interface to help to set up which bonds will treated as rotatable in the ligand and to analyze dockings. Used for automated docking with selective receptor flexibility. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure.
Proper citation: AutoDockTools (RRID:SCR_026401) Copy
https://ruggleslab.shinyapps.io/RIVET/
Software tool to automate statistical analysis of RNA seq data acquired from polysome profile or ribosome footprinting experiments.
Proper citation: RIVET (RRID:SCR_026488) Copy
https://www.janelia.org/support-team/immortalized-cell-line-culture
Core offers support for various tasks such as plating, passaging, cryopreserving, transfection, and preparing cells for imaging and other applications. Our facility fosters collaboration, allowing researchers to reserve cell culture hoods and engage with fellow lab and staff members.
Proper citation: Howard Hughes Medical Institute at Janelia Research Campus Immortalized Cell Line Culture Shared Resource Core Facility (RRID:SCR_026515) Copy
Provides services and instrumentation including Illumina Next-Generation Sequencing, Single Cell Analysis and Spatial Transcriptomics. These techniques are developed and optimized by our lab scientists to deliver the highest-possible quality sequencing data from a wide variety of sample types such as peripheral blood, bone marrow, fresh frozen tissue and FFPE-derived tumor samples.
Proper citation: University of Texas Institute for Personalized Cancer Therapy Cancer Genomics Laboratory Core Facility (RRID:SCR_026469) Copy
https://ecog-acrin.org/resources/ecog-performance-status/
ECOG Performance Scale describes patient’s level of functioning in terms of their ability to care for themself, daily activity, and physical ability (walking, working, etc.). Standard criteria for measuring how the disease impacts patient’s daily living abilities. Used to assess the functional status of patient.
Proper citation: Eastern Cooperative Oncology Group Performance Status Scale (RRID:SCR_026432) Copy
https://github.com/soedinglab/mmseqs2
Software suite to search and cluster huge protein and nucleotide sequence sets. Sensitive protein sequence searching for analysis of massive data sets. Used for ultra fast and sensitive search and clustering.
Proper citation: MMseq2 (RRID:SCR_026553) Copy
Open-source DataFrame library for data manipulation known for being one of the fastest data processing solutions on single machine. Features well-structured, typed API that is both expressive and easy to use. DataFrame interface on top of OLAP Query Engine implemented in Rust using Apache Arrow Columnar Format as the memory model.
Proper citation: Polars (RRID:SCR_026431) Copy
https://who-umc.org/whodrug/whodrug-global/
International reference guide for medicinal products maintained by the Uppsala Monitoring Centre. With its unique drug code hierarchy and extensive coverage, it provides consistent drug dictionary with exact terminology when coding concomitant medications. Dictionary is used to identify drug names and evaluate medicinal product information, including active ingredients and products’ anatomical and therapeutic classifications, from nearly 150 countries. Data covers both conventional medicines and herbal remedies. Data is continuously updated, with new releases twice a year, on 1 March and 1 September.
Proper citation: WHODrug Global (RRID:SCR_026433) Copy
https://tetramer.yerkes.emory.edu
Core produces and distributes of MHC/peptide tetramers and related reagents. Production and distribution to the research community of major histocompatibility complex (MHC) tetramers and related reagents for detection of T cell responses to viruses, bacteria, parasites, tumors, auto-antigens, and other model antigens. Reagents are provided to qualified investigators at no cost, except for shipping and handling fees and in cases where investigator is asked to provide the TCF with peptide or other appropriate ligands.
Proper citation: Emory University NIH Tetramer Core Facility (RRID:SCR_026557) Copy
https://www.mayo.edu/research/core-resources/spatial-biology-core/overview
Core provides broad range of spatial transcriptomic and targeted proteomics services including: Conventional nCounter analysis to determine RNA abundance, GeoMx Digital Spatial Profiling platform to determine protein and RNA abundance, CosMx Spatial Molecular Imaging platform for single cell spatial analysis of RNA and protein.
Proper citation: Mayo Clinic Spatial Biology Core Facility (RRID:SCR_026548) Copy
DNA synthesis company provides comprehensive services including gene synthesis, protein expression, gene editing, etc., supporting one-stop solutions for global users.
Proper citation: Synbio Technologies (RRID:SCR_026374) Copy
https://github.com/SoSongzhi/PVGA
Software tool as virus-focused assembler that does both assembly and polishing into unified workflow. Viral genome assembler enables detection of subtle genomic variations that can significantly impact viral function and pathogenicity.
Proper citation: PVGA (RRID:SCR_026410) Copy
https://github.com/compgenomics/MeTPeak
Software package for finding the location of m6A sites in MeRIP-seq data.
Proper citation: MeTPeak (RRID:SCR_026533) Copy
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