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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/CSB5/INC-Seq
Software for accurate single molecule reads using nanopore sequencing. Used for 16S rRNA-based profiling to investigate complex bacterial communities.
Proper citation: INC-Seq (RRID:SCR_016711) Copy
https://github.com/umerijaz/nanopore
Software for a workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform. Used for full-length SSU rRNA gene sequencing.
Proper citation: NanoAmpli-Seq (RRID:SCR_016710) Copy
http://jefferis.github.io/nat/
Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures.
Proper citation: NeuroAnatomy Toolbox (RRID:SCR_016716) Copy
http://biophysics.fsu.edu/facilities/physical-biochemistry-facility/
Facility for biophysical studies of macromolecules with emphasis on providing resources, instrumentation, training, and guidance to graduate and undergraduate students.
Proper citation: Florida State University Physical Biochemistry Core Facility (RRID:SCR_016714) Copy
Software package available through Fiji to image large biological specimen at high resolution. Comes with 2 different plugins to reconstruct big images/stacks : Pairwise Stitching to stitch two 2d-5d images, and Grid/Collection Stitching to stitch an arbitrary amount of 2d-5d input images.
Proper citation: Stitching (RRID:SCR_016568) Copy
https://molecular.pathology.ufl.edu/
Histology and light microscopy facility for paraffin and frozen blocks and all aspects of sample preparation, fixation, embedding, sectioning, staining, and imaging. Consultations, technical assistance and training are also provided. Standard operating procedures compliant with good laboratory and clinical processes are followed for all procedures. Services include cryosectioning, whole slide imaging, hematoxylin and eosin staining, immunfluorescence, and tissue microarrays..
Proper citation: University of FLorida College of Medicine Molecular Pathology Core Facility (RRID:SCR_016601) Copy
Software to provide control of the cell sorter from configuration and compensation setup to acquisition, sorting, and analysis, making it easy to customize the instrument for specific applications. BD implements software solutions that integrate data, devices and systems.
Proper citation: BD FACS Sortware sorter software (RRID:SCR_016722) Copy
Collection of disease maps, and mapped collection data and distribution models for arthropod disease vector species, including mosquitoes, ticks, sand flies, mites, and fleas, as well as the hosts/reservoirs of vector-borne disease pathogens. VectorMap is modeled after MosquitoMap.
Proper citation: VectorMap (RRID:SCR_016721) Copy
http://www.nbtltd.com/products/smi-begaze%E2%84%A2-analysis-software
Software package for eye tracking studies by New Bio Technology Ltd. Used for designing eye movement studies and recording, analyzing, visualizing data of eye tracking results.
Proper citation: SMI BeGaze (RRID:SCR_016648) Copy
http://projects.biotec.tu-dresden.de/metapocket/
Software tool to identify pockets on protein surface to predict ligand-binding sites.
Proper citation: metaPocket (RRID:SCR_016653) Copy
Software assembler and analysis tool for whole-genome short-gun sequencing for Illumina reads. Provides tools for error correction, sequence-to-read alignment and comparison between read sets. Used for large genomes.
Proper citation: fermi (RRID:SCR_016652) Copy
Software toolbox for MATLAB for the descriptive and inferential statistical analysis of directional data.
Proper citation: circular statistics (RRID:SCR_016651) Copy
Software tool for multi level analysis of applications optimized for ImageXpress instruments. High-content image analysis software featuring time lapse analysis. Used for 2D and 3D imaging.
Proper citation: MetaXpress (RRID:SCR_016654) Copy
Platform as a web-based interactive environment to automatically identify, explore and visualize homology and functional annotations for assembled transcripts.
Proper citation: Genotate (RRID:SCR_016659) Copy
https://github.com/WilsonSayresLab/XYalign
Software tool for identifying, understanding, and correcting technical biases on the sex chromosomes in next generation sequencing data.
Proper citation: XYalign (RRID:SCR_016661) Copy
Python implementation of the Loom file format to store and organize very large omics datasets, consisting of a main matrix, optional additional layers, a variable number of row and column annotations and sparse graph objects. Used to store single-cell gene expression data. Official Python library (API) used to create, read, and manipulate .loom files, supporting out-of-memory operations to handle datasets larger than RAM.
Proper citation: LoomPy (RRID:SCR_016666) Copy
http://www.ccb.jhu.edu/software/centrifuge/
Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers.
Proper citation: Centrifuge Classifier (RRID:SCR_016665) Copy
https://www.schrodinger.com/macromodel
Software package for molecular modeling. Computes free energy changes using free energy perturbation method. Used to examine molecular conformations, molecular motion, and intermolecular interactions, such as those in a ligand-receptor complex.
Proper citation: MacroModel (RRID:SCR_016747) Copy
Collection of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. Database and web applications support the storage, annotation, analysis, and exchange of information.
Proper citation: PaVE (RRID:SCR_016599) Copy
https://github.com/vaklip/transfer_learning_ccnn
Software program to implement transfer learning for a connectome convolutional neural network trained to classify functional connectomes using Tensorflow.
Proper citation: transfer_ learning_ ccnn (RRID:SCR_016590) Copy
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