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https://github.com/Nextomics/NextDenovo

Software error correction and accurate assembly tool for noisy long reads. De novo assembler for long reads. String graph-based de novo assembler for long reads like CLR, HiFi and ONT.

Proper citation: NextDenovo (RRID:SCR_025033) Copy   

•   Source: SciCrunch Registry

https://geom.kopflab.org/

Microbial culturing facility focused on growing microorganisms with diverse physiologies from photosynthesis to methanogenesis.

Proper citation: University of Colorado Boulder Geomicrobiology Lab Core Facility (RRID:SCR_025034) Copy   

•   Source: SciCrunch Registry

https://github.com/caaswxb/SRY

Software application for sorting long-read of sex-limited (Y or W) chromosome. Used to identify male specific k-mers based on population data.

Proper citation: Sorting long Reads of Y or other sex-limited chromosome (RRID:SCR_025036) Copy   

•   Source: SciCrunch Registry

https://www.wistar.org/our-science/shared-facilities/molecular-screening-protein-expression-facility

Facility enables to discover molecular, genetic, and small molecule compounds suitable to study functions of poorly understood proteins, signaling pathways, and cells in complex biological processes relevant to human physiology and disease; provides technical assistance with viral vector preparation and expression and purification of recombinant proteins; fosters collaborations. Staff will also develop and implement new technology as needed. Education and training is also available. Provides opportunities to develop new innovative basic and translational research, preliminary data for hypothesis driven research grant applications, and public-private partnerships.

Proper citation: Wistar Institute Molecular Screening and Protein Expression Core Facility (RRID:SCR_024978) Copy   

•   Source: SciCrunch Registry

https://data.ub.uni-muenchen.de/

Data publication platform for publication and hosting of research data. Data repository contains open access journals published at Ludwig-Maximillians University, Munich, Germany. Server provides direct access to research data sets produced by projects at LMU. Open Journals LMU. Open Data LMU.

Proper citation: Open Data LMU (RRID:SCR_025005) Copy   

•   Source: SciCrunch Registry

http://www.mikaia.ai

Software image analysis tool for digital pathology and spatial biology researchers.

Proper citation: MIKAIA (RRID:SCR_025081) Copy   

•   Source: SciCrunch Registry

https://scilab.stanford.edu/

Core for understanding Earth surface processes in bedrock, soil, water, and sediment. Interactions between cosmic rays and Earth’s upper atmosphere create unique isotopes both in the atmosphere and in materials on Earth’s surface. By assessing the ratios and/or concentrations of these isotopes, we can get a deeper insight into the exposure age, soil production rate, catchment-averaged erosion, and processes of Earth’s varied landscapes.

Proper citation: Stanford University Cosmogenic Isotope Lab Core Facility (RRID:SCR_025082) Copy   

•   Source: SciCrunch Registry

https://aging.ufl.edu/research/oaic-cores/systems-physiology-and-omics-core/

Provides specialized resources and expertise to support scientists that want to incorporate systemic measures of mouse activity, metabolism and feeding. The systems are also embedded within light regulated environments to capture circadian, time of day, based outcomes.Supports scientists wanting to perform circadian type analyses with either pre-clinical or clinical time series data. Supports scientists wanting to incorporate -Omics measures into their studies with experience in genomics, proteomics and metabolomics assays/analyses. These services are available to support new investigators, early-stage investigators and current investigators in aging.

Proper citation: University of Florida Systems Physiology and Omics Core Facility (RRID:SCR_025083) Copy   

•   Source: SciCrunch Registry

https://cancer.wisc.edu/research/resources/flow/

Facility provides technical and educational support for fluorescence based single cell analysis and isolation to further the characterization and understanding of cellular function, biomarkers, pathology, and treatment in basic, translational, and clinical research projects.

Proper citation: University of Wisconsin-Madison Carbone Cancer Center Flow Laboratory Core Facility (RRID:SCR_025085) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fslutils

Software application set of useful command line utilities which allow conversion, processing etc. of Analyze and Nifti format data sets.

Proper citation: Fslutils (RRID:SCR_024943) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlasquery

Software tool designed to allow command line interrogation of atlas images supplied with FSL. It takes as input the name of one of FSL atlases together with either coordinate of interest or mask.

Proper citation: Atlasquery (RRID:SCR_024944) Copy   

•   Source: SciCrunch Registry

https://github.com/bioinfodlsu/rice-pilaf

Web app for post-GWAS/QTL analysis that performs slew of novel bioinformatics analyses to cross GWAS/QTL mapping results with host of publicly available rice databases.

Proper citation: RicePilaf (RRID:SCR_024945) Copy   

•   Source: SciCrunch Registry

https://msgp.pt/

Database of protein components of mammalian stress granules.

Proper citation: Mammalian Stress Granules Proteome (RRID:SCR_024946) Copy   

•   Source: SciCrunch Registry

https://biotech.unl.edu/bioinformatics

Core offers education, analysis, and computational services in the area of bioinformatics and computational biology. Offers initial consultations to help with experimental design and power analysis of 'omics data for grant submissions and bioinformatics needs for current projects.

Proper citation: University of Nebraska Lincoln Bioinformatics Core Facility (RRID:SCR_025011) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/gensim/

Software Python library for unsupervised topic modeling, document indexing, retrieval by similarity, and other natural language processing functionalities, using modern statistical machine learning.

Proper citation: gensim (RRID:SCR_025099) Copy   

•   Source: SciCrunch Registry

https://github.com/BlankenbergLab/gmxtras/tree/main

Software tool as set of Python scripts to modify GROMACS topology files, by adding content from different topology files and other GROMACS input files. Useful, particularly when system components are assembled outside of GROMACS, or in different steps within GROMACS. This helps prevent users from having to copy and paste significantly large blocks of text within topology files.

Proper citation: GROMACS topology editors (RRID:SCR_025013) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/fast2q/

Software package for general purpose sequence search and counting program for FASTQ files. Python3 program that counts sequence occurrences in raw FASTQ files. Used for CRISPRi-Seq, and for extracting and counting any kind of information from Illumina reads, such as barcodes.

Proper citation: 2FAST2Q (RRID:SCR_025017) Copy   

•   Source: SciCrunch Registry

https://pycontact.github.io/

Software tool for analysis of non-covalent interactions in molecular dynamics trajectories. Implemented in Python and is universally applicable to any kind of MD trajectory supported by MDAnalysis package.

Proper citation: PyContact (RRID:SCR_025066) Copy   

•   Source: SciCrunch Registry

https://github.com/GreyGuoweiChen/VirHost

Software tool for predicting reservoir hosts of RNA viruses through viral genomes. Takes complete RNA viral genomes as input and predicts natural reservoir host groups from kingdom level to order level.

Proper citation: VirHost (RRID:SCR_025061) Copy   

•   Source: SciCrunch Registry

https://cancer.dartmouth.edu/scientists-researchers/irradiation-imaging-microscopy-animal-resource

Integrated core offers services in Irradiation, pre-clinical imaging of small and large animals, light and electron microscopy, large and small animal cancer models. Irradiation Section assists investigators in radiation treatment planning and delivery of ionizing irradiation to cells, rodents and large animals with engineered, transplanted or spontaneous tumors.Imaging Section provides technologies for non-invasive, whole-animal imaging of animals used in preclinical research studies. Microscopy Section provides access to point scanning confocal microscopy with Airyscan super resolution, conventional bright field and fluorescence light microscopy, high throughput live imaging, automated slide scanning and image analysis resources. Electron microscopy resource provides scanning transmission electron microscopy. Animal Cancer Models section supports generation and utilization of large and small animals for modeling cancer and other human diseases. Section has expertise in generating cancer models using wild type or genetically engineered animals in immunocompetent and immunocompromised backgrounds, as well as mice with humanized immune system.

Proper citation: Geisel School of Medicine at Dartmouth DCC Irradiation, Imaging, Microscopy and Animal Cancer Models Core Facility (RRID:SCR_025077) Copy   

•   Source: SciCrunch Registry