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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/powellgenomicslab/ascend
Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions.
Proper citation: ascend (RRID:SCR_017257) Copy
https://proteomics.cancer.gov/programs/cptac
Clinical proteomic tumor analysis consortium to systematically identify proteins that derive from alterations in cancer genomes and related biological processes, in order to understand molecular basis of cancer that is not possible through genomics and to accelerate translation of molecular findings into clinic. Operates through Proteome Characterization Centers, Proteogenomic Translational Research Centers, and Proteogenomic Data Analysis Centers. CPTAC investigators collaborate, share data and expertise across consortium, and participate in consortium activities like developing standardized workflows for reproducible studies.
Proper citation: CPTAC (RRID:SCR_017135) Copy
Software tool as stochastic algorithm for estimating maximum likelihood phylogenies. Used for phylogenomic inference.
Proper citation: IQ-TREE (RRID:SCR_017254) Copy
http://research.mssm.edu/integrative-network-biology/Software.html
Software tool as probabilistic multi omics data matching procedure to curate data, identify and correct data annotation and errors in large databases. Used to check potential labeling errors in profiles where number of cis relationships is small, such as miRNA and RPPA profiles.
Proper citation: proMODMatcher (RRID:SCR_017219) Copy
http://sehilyi.com/mirtarvisplus/
Web based interactive visual analytics tool for miRNA target predictions and integrative analyses of multiple prediction results. Used for sequence based miRNA target prediction by exploiting miRNA-mRNA expression profile data.
Proper citation: miRTarVisPlus (RRID:SCR_017103) Copy
https://github.com/FeeLab/seqNMF
Software tool for unsupervised discovery of sequential structure. Used to detect sequences in neural data generated by internal behaviors, such as animal thinking or sleeping. Used for unsupervised discovery of temporal sequences in high dimensional datasets in neuroscience without reference to external markers.
Proper citation: seqNMF (RRID:SCR_017068) Copy
https://cf.gu.se/english/bioinformatics
Core assists with statistical and bioinformatics consultation and data analysis.
Proper citation: University of Gothenburg Bioinformatics Core Facility (RRID:SCR_017189) Copy
Portal to provide integrated and federated system that interconnects diverse microbiome data sets, bioinformatics tools, and community resources. Built on guiding principles for FAIR data. Open source, community driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with broader community. Partners with CyVerse and XSEDE.
Proper citation: iMicrobe (RRID:SCR_017108) Copy
https://www.datasci.com/products/software/ponemah
Software tool for complete physiologic data acquisition and analysis used by physiologists, pharmacologists, and toxicologists to collect, analyze, and summarize preclinical study data. Allows to custom design configuration based on needs, budget and convenience without need for any programming.
Proper citation: Ponemah (RRID:SCR_017107) Copy
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
Organize, Store, Disseminate, Analyze and Visualize Invasive Neurophysiology Data. Shared archive and resource for human invasive neurophysiology data that have been established by Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative along with software tools for data uploading, visualization and analysis. Users can view and query datasets through online interface but cannot access raw data. Platform utilizes centralized and federated model. Investigators may upload data to central archive or house it themselves.
Proper citation: Data Archive BRAIN Initiative (RRID:SCR_017114) Copy
Web application for Quantitative Trait Loci mapping via bulk segregant analysis of yeast sequencing data. Application provides automated data processing, annotations, and web interface to explore identified QTLs.
Proper citation: BSA4Yeast (RRID:SCR_017113) 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://github.com/tseemann/shovill
Software tool to assemble bacterial isolate genomes from Illumina paired end reads. Used for isolate data only, primarily small haploid organisms. Supports assemblers like SKESA, Velvet and Megahit.
Proper citation: shovill (RRID:SCR_017077) Copy
https://inutano.github.io/cwl-metrics/
Software framework to collect and analyze computational resource usage of workflow runs based on common workflow language CWL. Used to share set of tools packaged in containers. Enables users to choose proper cloud instance for workflow runs based on run time metrics data. Operating system Unix/Linux.
Proper citation: cwl-metrics (RRID:SCR_017076) Copy
Provides assistance in computing, nanotechnology, and biological fields. Provides scientific support and resources to the UMA research groups, public institutions and private companies.
Proper citation: University of Malaga Andalusian Platform of Bioinformatics Core Facility (RRID:SCR_017169) Copy
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