Tools   Select Another Resource Report Type

https://data.broadinstitute.org/alkesgroup/BOLT-LMM/

Software statistical tool for identifying genetic associations. Used for genome wide association studies in large cohorts.

Proper citation: BOLT-LMM (RRID:SCR_023978) Copy   

•   Source: SciCrunch Registry
  

https://www.illumina.com/systems/sequencing-platforms/nextseq-1000-2000.html

Sequencing system supports range of methods such as exome sequencing, target enrichment, single-cell profiling.

Proper citation: Illumina: NextSeq 2000 system (RRID:SCR_023614) Copy   

•   Source: SciCrunch Registry
  

https://quint-workflow.readthedocs.io/en/latest/QUINTintro.html

Software workflow includes suite of various software to form analysis pipeline of atlas-based quantifuication of labbeled features in histological images from mouse or rat brain. This workflow also suggests and explains with instructional videos the way these software work together. Used for quantification and spatial analysis of labelling in series of rodent brain section images based on available 3D reference atlases.

Proper citation: QUINT (RRID:SCR_023856) Copy   

•   Source: SciCrunch Registry
  

https://www.ionpath.com/mibiscope/

Imaging platform, enabling phenotypic profiling and spatial analysis of tissue microenvironment. Enables over 40 markers to be visualized simultaneously with single step staining and single step imaging.

Proper citation: Ionpath: MIBIscope System (RRID:SCR_023613) Copy   

•   Source: SciCrunch Registry
  

https://www.htximaging.com/htx-m5-sprayer

Sprayer builds on capabilities of HTX TM-Sprayer providing innovative M5 chassis, high velocity stage and heated sample holder drawer. Sample plate holder is mounted on drawer mechanism to allow easy loading of samples, better protection of user and better alignment of various plate types. New High-Velocity XY stage allows nozzle displacement speed of up to 5,600mm/min and expands process range. Super dry spray can be achieved at high flow rates of solvent further improving instrument performance. E/Z trough gutter design improves chemical containement and is easy to remove and clean. Bulkhead connectors are directly mounted on it to also allow easy access to in line filter.

Proper citation: HTXImaging: M5 Sprayer (RRID:SCR_023733) Copy   

•   Source: SciCrunch Registry
  

https://www.htximaging.com/tm-sprayer

Allows users to adjust both gas flow rate and nozzle velocity to control drying time, preventing analyte delocalization and formation of large matrix crystals, known to create hot spots on MALDI images. Allows to heat matrix solution as it is being applied to their sample. By increasing temperature of matrix solution, absorption of matrix into sample is increased, resulting in greater MALDI image resolution.

Proper citation: HTXImaging: TM-Sprayer (RRID:SCR_023732) Copy   

•   Source: SciCrunch Registry
  

https://github.com/brainglobe/brainreg-segment

Software tool for manual segmentation of regions/objects within the brain. Brainreg-segment will only work if the user registers their data with brainreg first. Used for segmentation of 3D shapes in common anatomical space.

Proper citation: Brainreg-segment (RRID:SCR_023853) Copy   

•   Source: SciCrunch Registry
  

https://andor.oxinst.cn/products/scmos-camera-series/zyla-4-2-scmos

Zyla 4.2 PLUS is the latest sCMOS technology advancement from Andor. At its heart, Zyla 4.2 PLUS benefits from latest generation sCMOS sensor technology, delivering a further 10 % boost in QE, resulting in an unprecedented 82% QEmax.

Proper citation: Andor: Zyla 4.2 sCMOS (RRID:SCR_023610) Copy   

•   Source: SciCrunch Registry
  

https://www.htximaging.com/htx-m3-sprayer

Sample preparation platform offering automated advanced MALDI matrix sprayer.

Proper citation: HTXImaging: M3+ Sprayer (RRID:SCR_023731) Copy   

•   Source: SciCrunch Registry
  

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

Software R package with several tools for microbiome data analysis.

Proper citation: mia (RRID:SCR_023619) Copy   

•   Source: SciCrunch Registry
  

https://www.thermofisher.com/us/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-systems/orbitrap-lc-ms/orbitrap-tribrid-mass-spectrometers/orbitrap-eclipse-tribrid-mass-spectrometer.html

Mass spectrometer designed for most difficult analytical challenges. Incorporates inventions in ion transmission and control, extended m/z range, and real-time decision making. System suited for proteomics, structural biology, small-molecule, and biopharmaceutical characterization experiments.

Proper citation: Thermo Fisher: Orbitrap Eclipse Tribrid mass spectrometer (RRID:SCR_023618) Copy   

•   Source: SciCrunch Registry
  

https://github.com/sanger-pathogens/iva

Software tool as de novo assembler designed to assemble virus genomes that have no repeat sequences,using Illumina read pairs sequenced from mixed populations at extremely high and variable depth.

Proper citation: IVA (RRID:SCR_024044) Copy   

•   Source: SciCrunch Registry
  

https://www.cancergenomeinterpreter.org/home

Platform that systematizes interpretation of cancer genomes and makes it automatic. Web tool to annotate genomic alterations and interpret their possible role in tumorigenesis and in response to anti cancer therapies. Used to support identification of tumor alterations that drive disease and/or which may be therapeutically actionable. Analyses mutations including single nucleotide changes and small insertions/deletions, copy number alterations including gene amplifications and deletions and translocations.

Proper citation: Cancer Genome Interpreter (RRID:SCR_023752) Copy   

•   Source: SciCrunch Registry
  

http://contra.stanford.edu/contrafold/

Software novel secondary structure prediction method based on conditional log-linear models, a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. Used for sequence prediction.

Proper citation: CONTRAfold (RRID:SCR_023994) Copy   

•   Source: SciCrunch Registry
  

http://ingenium.home.xs4all.nl/dicom.html

Software for DICOM training and testing,Demonstration and research image archives,Image format conversion from scanner with DICOM network access,DICOM image viewing and slide making, DICOM image selection, (limited) editing, and splitting and merging of series, Advanced scriptable image modification, filtering, forwarding and conversion, DICOM caching and archive merging, DICOM web access for viewing and data management (scriptable),Connection to Lua IDE for all sorts of DICOM manipulation.

Proper citation: Conquest DICOM (RRID:SCR_023993) Copy   

•   Source: SciCrunch Registry
  

https://www.viewpoint.fr/product/zebrafish/cardiology/microzebralab

Software tool to extract cardiovascular parameters from transmitted light videos of zebrafish embryos or larvae. Used to investigate live and in non-invasive way scope of zebrafish larvae physiological parameters. Measures heartbeat and blood flow.

Proper citation: ViewPoint MicroZebraLab (RRID:SCR_023750) Copy   

•   Source: SciCrunch Registry
  

http://www.mircode.org/

Web tool for transcriptome wide microRNA target prediction including lncRNAs.Used for whole transcriptome human microRNA target predictions based on the comprehensive GENCODE gene annotation, including long non-coding RNA genes. Coding genes are also covered, including atypical regions such as 5'UTRs and CDS. MicroRNA family definitions and names are consistent with TargetScan. Site conservation is aluated based on 46 vertebrates species.Map of putative microRNA target sites in the long non-coding transcriptome.

Proper citation: miRCode (RRID:SCR_023870) Copy   

•   Source: SciCrunch Registry
  

https://github.com/omnideconv/immunedeconv

Software R package for unified access to computational methods for estimating immune cell fractions from bulk RNA sequencing data.

Proper citation: Immunedeconv (RRID:SCR_023869) Copy   

•   Source: SciCrunch Registry
  

http://tiger.bsc.es

Resource enables integrative exploration of genetic and epigenetic basis of development of Type 2 Diabetes, together with other associated functional, molecular and clinical data, centered in biology and role of pancreatic beta cells.The gene expression regulatory variation landscape of human pancreatic islets.

Proper citation: TIGER Data Portal (RRID:SCR_023626) Copy   

•   Source: SciCrunch Registry
  

https://www.zeiss.com/microscopy/en/products/software/zeiss-zen-lite.html

Software tool for basic image acquisition and analysis. Zeiss ZEN microscopy software to control of axiocam microscope cameras, image transformation and measurements, image processing, image alignment for correlative microscopy, various visualization options.

Proper citation: Zeiss Zen Lite (RRID:SCR_023747) Copy   

•   Source: SciCrunch Registry