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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/aidenlab/juicer.git
Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps.
Proper citation: Juicer (RRID:SCR_017226) Copy
https://github.com/anaphaze/ot-tools
Software tools for analysis of cellular cryo-ET data.
Proper citation: ot-tools (RRID:SCR_017191) Copy
http://www.igc.gulbenkian.pt/facilities/bioinformatics
IGC Core in Oeiras, Portugal, promotes use of computational methods in biological research, through training and development of resources and materials, supports biological data analysis using computational methods, conducts research and development in bioinformatics, in particular in data flows, data warehousing and data analyses.
Proper citation: Gulbenkian Institute of Science Bioinformatics and Computational Unit Core Facility (RRID:SCR_017190) Copy
https://www.ed.ac.uk/igmm/facilities/bioinformatics-analysis-core
Core provides advice, training, provision of computational tools and collaborative expertise to all IGMM researchers.
Proper citation: University of Edinburgh College of Medicine and Veterinary Medicine MRC Institute of Genetics and Molecular Medicine Bioinformatics Analysis Core Facility (RRID:SCR_017194) Copy
https://www.a-star.edu.sg/gis/Our-Science/Technology-Platforms/Scientific-and-Research-Computing
Core provides research computing resources including bioinformatics, application development, data management and IT infrastructure to support next generation sequencing technologies, human genotyping, high throughput screening and computational biology researchers.
Proper citation: Genome Institute of Singapore Scientific and Research Computing Core Facility (RRID:SCR_017193) Copy
https://www.trophoblast.cam.ac.uk/Resources/BioInformatics
Core provides assistance with experimental design, RNA sequencing, whole genome and targeted sequencing, methylation sequencing, protein alignment, microscopy image analysis, and training.
Proper citation: University of Cambridge Centre for Trophoblast Research Bioinformatics Core Facility (RRID:SCR_017192) Copy
https://www.keyence.co.jp/products/microscope/fluorescence-microscope/bz-8100/models/bz-h1a/
Software tool as analysis application BZ-H1A by Keyence, Japan for fluorescence microscope BZ-8100 series.
Proper citation: BZ Analyzer software (RRID:SCR_017205) Copy
http://relacs.sourceforge.net/
Software platform for closed loop data acquisition, online analysis, and stimulus generation specifically designed for, but not limited to, electrophysiological recordings.
Proper citation: Relacs (RRID:SCR_017280) Copy
https://www.mbfbioscience.com/vesselucida360
Software tool for visualization and automatic reconstruction of microvascular networks in 3D environment with built-in analysis tools by MBF Bioscience.
Proper citation: Vesselucida 360 (RRID:SCR_017320) Copy
Software tool for automated removal of spurious sequences or poorly aligned regions from multiple sequence alignment. Software package for automated alignment trimming in large scale phylogenetic analyses.
Proper citation: trimAl (RRID:SCR_017334) Copy
https://arxiv.org/abs/1308.2012
Software tool for estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Used as general and assembly independent method for estimating genomic characteristics.
Proper citation: GCE (RRID:SCR_017332) Copy
https://www.beckman.it/flow-cytometry/research-flow-cytometers/cytoflex/software
Software program that controls instrument operation, data collection and analysis. Software for CytoFLEX Platform by Beckman Coulter.
Proper citation: CytExpert Software (RRID:SCR_017217) Copy
https://github.com/EpistasisLab/pennai
Open source software tool to leverage supervised machine learning techniques to analyze data. Can assist with tasks such as choosing appropriate models for data. Data science assistant for generating results from large and complex data problems.
Proper citation: PennAI (RRID:SCR_017215) Copy
https://www.cmrr.umn.edu/downloads/mrspa
Software package to post process MR spectroscopy data. Magnetic Resonance signal processing and analysis software. Runs under Matlab.
Proper citation: MRspa (RRID:SCR_017292) Copy
https://ircm.qc.ca/en/technological-services/bioinformatics
Core to support scientists within and outside IRCM in analysis of biological and clinical data, in particular high throughput genomic data. Operating on collaborative basis and paid services. Provides assistance with Data analysis for RNA-Seq, ChIP-Seq, RIP-Seq, DNA methylation, DNA-Seq, targeted sequencing of rRNAs, microarrays, customized training courses.
Proper citation: Montreal Clinical Research Bioinformatics Core Facility (RRID:SCR_017176) Copy
Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager.
Proper citation: BEAST2 (RRID:SCR_017307) Copy
https://github.com/ISUgenomics/SequelQC
Software tool that calculates key statistics and generates publication quality plots for raw PacBio Sequel data. Open source software for analyzing PacBio Sequel raw sequence data.
Proper citation: SequelQC (RRID:SCR_017279) Copy
Software tool for data analysis and scientific visualization by IONDEV SRL.
Proper citation: QtiPlot (RRID:SCR_017311) Copy
Software JAVA based application for basic analysis of Small Angle X-ray Scattering datasets.
Proper citation: SCÅTTER (RRID:SCR_017271) Copy
https://deepblue.mpi-inf.mpg.de/
Central data access hub for large collections of epigenomic data. It organizes data from different sources using controlled vocabularies and ontologies. Data Server for storing, organizing, searching, and retrieving genomic and epigenomic data, handling associated metadata, and to perform different types of analysis.
Proper citation: Deep Blue Epigenomic Data Server (RRID:SCR_017490) Copy
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