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https://bioconductor.org/packages/release/bioc/html/Maaslin2.html

SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features.

Proper citation: MaAsLin2 (RRID:SCR_023241) Copy   

•   Source: SciCrunch Registry

https://github.com/virajbdeshpande/AmpliconArchitect

Software package designed to call circular DNA from short read WGS data.Used to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates architecture of amplicon.Used to reconstruct structure of focally amplified regions using whole genome sequencing and validate it extensively on multiple simulated and real datasets, across wide range of coverage and copy numbers.

Proper citation: AmpliconArchitect (RRID:SCR_023150) Copy   

•   Source: SciCrunch Registry

https://github.com/compbiolabucf/omicsGAN

Software generative adversarial network to integrate two omics data and their interaction network to generate one synthetic data corresponding to each omics profile that can result in better phenotype prediction. Used to capture information from interaction network as well as two omics datasets and fuse them to generate synthetic data with better predictive signals.

Proper citation: OmicsGAN (RRID:SCR_022976) Copy   

•   Source: SciCrunch Registry

http://virusdetect.feilab.net/cgi-bin/virusdetect/index.cgi

Software package to efficiently and exhaustively analyze large scale sRNA datasets for virus identification. Automated pipeline for virus discovery using deep sequencing of small RNAs.

Proper citation: VirusDetect (RRID:SCR_023669) Copy   

•   Source: SciCrunch Registry

https://rockd.org/

Map database allows to record your geological observations and uses your location to provide spatially informed suggestions for nearby geologic units, time intervals, and fossils.

Proper citation: rockd (RRID:SCR_024431) Copy   

•   Source: SciCrunch Registry

http://www.ldeo.columbia.edu/core-repository

Core repository and one of the world's most unique and important collections of scientific samples from the deep sea. Sediment cores from every major ocean and sea are archived at the Core Repository. The collection contains approximately 72,000 meters of core composed of 9,700 piston cores; 7,000 trigger weight cores; and 2,000 other cores such as box, kasten, and large diameter gravity cores. They also hold 4,000 dredge and grab samples, including a large collection of manganese nodules, many of which were recovered by submersibles. Over 100,000 residues are stored and are available for sampling where core material is expended. In addition to physical samples, a database of the Lamont core collection has been maintained for nearly 50 years and contains information on the geographic location of each collection site, core length, mineralogy and paleontology, lithology, and structure, and more recently, the full text of megascopic descriptions. Samples from cores and dredges, as well as descriptions of cores and dredges (including digital images and other cruise information), are provided to scientific investigators upon request. Materials for educational purposes and museum displays may also be made available in limited quantities when requests are adequately justified. Various services and data analyses, including core archiving, carbonate analyses, grain size analyses, and RGB line scan imaging, GRAPE, P-wave velocity and magnetic susceptibility runs, can also be provided at cost. The Repository operates a number of labs and instruments dedicated to making fundamental measurements on material entering the repository including several non-destructive methods. Instruments for conducting and/or assisting with analyses of deep-sea sediments include a GeoTek Multi-Sensor Core Logger, a UIC coulometer, a Micromeritics sedigraph, Vane Shear, X-radiograph, Sonic Sifter, freeze dryer, as well as a variety of microscopes, sieves, and sampling tools. They also make these instruments available to the scientific community for conducting analyses of deep-sea sediments. If you are interested in borrowing any field equipment, please contact the Repository Curator.

Proper citation: Lamont-Doherty Core Repository (RRID:SCR_002216) Copy   

•   Source: SciCrunch Registry

http://lrc.geo.umn.edu/laccore/

Archive of almost 20,000 meters of high quality sediment cores from large and small expeditions to lakes all around the world. LacCore advocates for, coordinates, and facilitates core-based research on Earth's continents through collaborative support for logistics, field and laboratory, and data and sample curation and dissemination. They provide a wide variety of fee-based analytical services, as well as offer training and instrument time to lab visitors. They also develop Standard Operating Procedures (SOPs) for local training and adoption by individuals at other labs.

Proper citation: National Lacustrine Core Facility (RRID:SCR_002215) Copy   

•   Source: SciCrunch Registry

https://nationalmaglab.org/user-facilities/high-b-t-facility

Facility to conduct experiments in high magnetic fields up to 15 tesla and at very low temperatures down to 0.4 mK simultaneously. Located at University of Florida in Gainesville, it is operated as part of Physics Department Microkelvin Laboratory.

Proper citation: National High Magnetic Field Laboratory High B/T Core Facility (RRID:SCR_017360) Copy   

•   Source: SciCrunch Registry

https://amris.mbi.ufl.edu/

National High Magnetic Field Laboratory (MagLab) site. It provides researchers with advanced NMR, MRI, and spectroscopy tools (human/animal imaging) for biomedical studies, specializing in high-field magnetic resonance technology. Hosts spectrometers and scanners, including high-field NMR (up to 1.5 GHz), MR microscopy, and human/animal MRI systems (e.g., 3T and 900 MHz). Offers expertise in high-resolution solution NMR, solid-state NMR, and specialized imaging for in vivo animal models and humans.Features an RF coil lab that designs, builds, and tests custom MRI/NMR coils to optimize data collection. Supports research into Alzheimer's, cancer, metabolism, and brain development.

Proper citation: National MagLab University of Florida McKnight Brain Institute Advanced Magnetic Resonance Imaging and Spectroscopy AMRIS Core Facility (RRID:SCR_017362) Copy   

•   Source: SciCrunch Registry

http://bioimaging.dbi.udel.edu

Microscopy facility that houses equipment including confocal microscopes: LSM780 confocal microscope (Located at CBBI),LSM880 confocal microscope (Located at DBI 117),electron microscopes and their accessory instrumentation:Thermo Scientific Apreo VS SEM microscope,Hitachi S-4700, Leica EM ACE600 and Tousimis Autosamdri-815B,CX7 high content analysis system. Our staff has technical expertise across different microscopy platforms and methodologies.

Proper citation: University of Delaware BioImaging Center Core Facility (RRID:SCR_017814) Copy   

•   Source: SciCrunch Registry

http://www.udel.edu/chem/beebe/surface.htm

Core provides consulting and services in X-ray Photoelectron Spectroscopy (XPS or ESCA), Time-of-Flight Secondary-Ion Mass Spectrometry (TOF-SIMS), X-ray Photoelectron Imaging, Auger Electron Spectroscopy (AES), Scanning Auger Microscopy or Imaging (SAM), Secondary-Electron Microscopy (SEM), Ion-Scattering Spectroscopy (ISS or LEIS), Scanning Probe Microscopy (STM and AFM).

Proper citation: Delaware University Surface Analysis Core Facility (RRID:SCR_017796) Copy   

•   Source: SciCrunch Registry

https://www.mccormick.northwestern.edu/materials-science/clammp/

Core provides mechanical testing machines and accessories for conducting educational, research, and outreach experiments on most solid materials.

Proper citation: Northwestern University Central Laboratory for Materials Mechanical Properties Core Facility (RRID:SCR_017877) Copy   

•   Source: SciCrunch Registry

http://crl.berkeley.edu/molecular-imaging-center/

Microscopy core specializing in laser based fluorescence techniques. Offers training and expertise in 20 different microscope systems, including live cell and in vivo imaging, laser scanning (LSM) and spinning disk (SDC) confocal, multi-photon (2p), fluorescent lifetime imaging (FLIM), light-sheet microscopy (SPIM), super resolution (Airyscan), slide scanning and patterned illumination for optogenetic manipulation and readout. Provides offline computer analysis workstations for image processing, visualization and analysis, including GPU workstations. MIC operates in 3 different buildings on campus, with primary locations in Life Sciences Addition (LSA), North-side core in Barker Hall, and small outpost in Li Ka Shing Center for Biomedical and Health Sciences (LKS).Provides equipment in categories:Confocal and multi photon laser scanning microscopes,Spinning disk confocal microscopes,Lightsheet (SPIM) microscopes,Epifluorescence/widefield scopes and Computer workstations.

Proper citation: University of California at Berkeley Cancer Research Laboratory Molecular Imaging Center Core Facility (RRID:SCR_017852) Copy   

•   Source: SciCrunch Registry

https://pynwb.readthedocs.io/en/latest/

Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information.

Proper citation: PyNWB (RRID:SCR_017452) Copy   

•   Source: SciCrunch Registry

https://github.com/sqjin/CellChat

Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets.

Proper citation: CellChat (RRID:SCR_021946) Copy   

•   Source: SciCrunch Registry

http://www.scrible.com/#desktop

We''re bringing Web-based research into the Internet Era by empowering people to mark up web pages in the browser and manage and collaborate on them online. And that''s just the start... We''ve got much more planned in a variety of areas to help people manage the mounds of info they''re pulling off the Web everyday. Simply drag the scrible bookmarklet to your browser''s Bookmarks toolbar. Click it later to mark up, save or share web pages. Even though the world uses the Internet to research nearly everything for work, school and home (job postings, press releases, Wikipedia articles, medical info, etc.), most folks still use old-school ways of annotating, organizing and sharing online info (printing to mark by hand, copying/pasting into Word, etc.). It''s archaic, laborious and a waste of time. We''re changing that. A bookmarklet is a bookmarked link that, when clicked, adds functionality to your browser. When the scrible Bookmarklet is clicked, it loads the scrible Toolbar atop the current webpage you''re viewing. Adding the scrible Bookmarklet to your browser is a breeze. Simply drag it to your browser''s Bookmarks Toolbar.

Proper citation: scrible (RRID:SCR_008882) Copy   

•   Source: SciCrunch Registry

http://www3.isrl.uiuc.edu/~TeleNature/bibe/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A facility to help novices and experts find information about plants and animals in digital collections. The objectives of the Project are to facilitate access to online flora and fauna by both novices and experts through enhanced indexing, searching, and visualization techniques. Specific search facility and content will be added to help users with different levels of domain knowledge identify species based on the augmentation of professionally developed taxonomic treatments or species descriptions. This is a novel use of taxonomic descriptions.

Proper citation: Biological Information Browsing Environment (RRID:SCR_008170) Copy   

•   Source: SciCrunch Registry

http://trex.biohpc.org/

T-REX is a free, platform-independent online tool that allows for an integrated, rapid, and more robust analysis of T-RFLP data. Despite increasing popularity and improvements in terminal restriction fragment length polymorphism (T-RFLP) and other microbial community fingerprinting techniques, there are still numerous obstacles that hamper the analysis of these datasets. Many steps are required to process raw data into a format ready for analysis and interpretation. These steps can be time-intensive, error-prone, and can introduce unwanted variability into the analysis. Accordingly, we developed T-REX, free, online software for the processing and analysis of T-RFLP data. Analysis of T-RFLP data generated from a multiple-factorial study was performed with T-REX. With this software, we were able to i) label raw data with attributes related to the experimental design of the samples, ii) determine a baseline threshold for identification of true peaks over noise, iii) align terminal restriction fragments (T-RFs) in all samples (i.e., bin T-RFs), iv) construct a two-way data matrix from labeled data and process the matrix in a variety of ways, v) produce several measures of data matrix complexity, including the distribution of variance between main and interaction effects and sample heterogeneity, and vi) analyze a data matrix with the additive main effects and multiplicative interaction (AMMI) model.

Proper citation: T-REX (RRID:SCR_010715) Copy   

•   Source: SciCrunch Registry

http://www.cravat.us/

A web-based application designed with an easy-to-use interface to facilitate the high-throughput assessment and prioritization of genes and missense alterations important for cancer tumorigenesis.

Proper citation: CRAVAT (RRID:SCR_012776) Copy   

•   Source: SciCrunch Registry

https://github.com/danbider/lightning-pose

Software video centric package for direct video manipulation. Semi supervised animal pose estimation algorithm, Bayesian post processing approach and deep learning package. Improved animal pose estimation via semi-supervised learning, Bayesian ensembling, and cloud-native open-source tools.

Proper citation: Lightning Pose (RRID:SCR_024480) Copy   

•   Source: SciCrunch Registry