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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.
http://www.biomedicumgenomics.fi/
Organization that provides academic and industrial clients access to functional genomics technologies, services and partnering solutions including genome-wide expression, copy number profiling, miRNA expression, DNA-protein interaction (ChIP-on-chip), Illumina high-throughput sequencing including nucleic acid quality and quantity assessment. For gene silencing and ectopic expression purposes, they offer high-titer shRNA and ORF lentiviruses targeting genes of interest. They also offer customized services e.g. preparation of gain or loss-of-function cell lines and protein interactomics-based services (yeast two-hybrid). In addition, they provide access to wide array of computational data analyses. BMGen also offers partnering deals for clients interested in customized integration of several technologies.
Proper citation: Biomedicum Genomics (RRID:SCR_003907) Copy
A Swiss service and consulting company specialized in the computational analysis of biomarker data from clinical trials. Their technical expertise spans across multiple biomaker technological platforms such as genetics, transcriptomics, protein assays and cellular assays. Quartz Bio is a spin-off of Merck Serono with the capital of the company entirely owned by its employees.
Proper citation: Quartz Bio (RRID:SCR_003919) Copy
http://watson.nci.nih.gov/bioc_mirror/packages/2.11/bioc/html/EDASeq.html
Software for numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).
Proper citation: EDASeq (RRID:SCR_006751) Copy
Bioanalyzer system is automated electrophoresis tool that providesa analytical evaluation of various samples types in many workflows, including next generation sequencing NGS, gene expression, biopharmaceutical, and gene editing research. Digital data is provided in timely manner and delivers assessment of sizing, quantitation, integrity and purity from DNA, RNA, and proteins. Minimal sample volumes are required for accurate result, and data may be exported in many different formats.
Proper citation: Agilent 2100 Bioanalyzer Instrument (RRID:SCR_018043) Copy
Database for evolutionary biochemical studies of caspase functional divergence and ancestral sequence inference. Tool to rapidly disseminate organized caspase sequence data. Includes all animal species with currently available annotated genomes in NCBI genome database. Manually curated and not curated sequences are available to download.
Proper citation: CaspBase (RRID:SCR_018975) Copy
https://wistar.org/research-discoveries/shared-resources/bioinformatics-facility
Core provides High Throughput Data Analysis, Customized Bioinformatics Services, Custom Programming, High Performance Computing, Data management. Located in the Center for Systems and Computational Biology. Provides Cancer Center investigators with database management, software application support, expertise in statistical analyses and computational modeling of biomedical research data.
Proper citation: Wistar Bioinformatics Core Facility (RRID:SCR_010203) Copy
http://www.scienceexchange.com/facilities/applied-bioinformatics-core
THIS RESOURCE IS NO LONGER IN SERVICE, documented January 23, 2019. Core supports SBMRI investigators in exploring, understanding and analyzing complex biological data. Core is equipped with cutting-edge computational infrastructure and a selective collection of bioinformatics software. Core's services include consultation, data analysis and management, software development, and accessing to large computing resources. To meet various demands from the investigators, we provide services at multiple levels, from full service to cost-effective limited service as well as collaborative projects requiring longer-term commitment of time and effort.
Proper citation: Sanford-Burnham Applied Bioinformatics Core Facility (RRID:SCR_012208) Copy
http://www.lji.org/faculty-research/scientific-cores/bioinformatics/#overview
Core Facility provides support for short or long-term projects requiring expertise the analysis of biological datasets. The services provided include the analysis of large-scale datasets (e.g. next-gen sequencing data, microarrays, etc.), the development of customized databases and reusable analysis pipelines, guidance on experimental design, support with technical sections of manuscripts and grants, and training on analysis software packages. All services are charged at our hourly rate.
Proper citation: La Jolla Institute for Allergy and Immunology Bioinformatics Core Facility (RRID:SCR_014831) Copy
https://en.freedownloadmanager.org/Windows-PC/Flowing-Software-FREE.html
Software for flow cytometry data analysis. Flowing Software has many common analysis tools, such as dot plots, histograms, quadrants, statistics, overlay histograms etc.
Proper citation: Flowing Software 2.5.1 (RRID:SCR_015781) Copy
Matlab toolbox that makes it easy to apply decoding analyses to neural data. The design of the toolbox revolves around four abstract object classes which enables users to interchange particular modules in order to try different analyses while keeping the rest of the processing stream intact. The toolbox is capable of analyzing data from many different types of recording modalities, and examples are given on how it can be used to decode basic visual information from neural spiking activity and how it can be used to examine how invariant the activity of a neural population is to stimulus transformations.
Proper citation: Neural Decoding Toolbox (RRID:SCR_009012) Copy
http://www.functionalglycomics.org/static/consortium/consortium.shtml
The Consortium for Functional Glycomics (CFG) serves to combine the expertise and glycomics resources to reveal functions of glycans and glycan-binding proteins (GBPs) that impact human health and disease. The CFG offers resources to the community free of charge, including glycan array screening services, a reagent bank, and access to a large glycomics database and data analysis tools.
Proper citation: Consortium for Functional Glycomics (CFG) (RRID:SCR_013689) Copy
A web application which allows users to collect data, perform complex analyses, and generate results. Users can upload data sets from their computer or from the internet for data analysis and graph creation which can be saved, printed, and downloaded. More than 15,000 statistical data sets are available.
Proper citation: StatCrunch (RRID:SCR_013992) Copy
A web application which performs Python data analysis. Users can create IPython notebooks to hold uploaded data and use various tools to describe, analyze, and visualize the data. Notebooks, data, and Anaconda environments can be shared as "bundles" with other users, who can edit and download them.
Proper citation: Wakari (RRID:SCR_013995) Copy
http://www.nitrc.org/projects/aperture/
A MATLAB-based toolbox for analysis of EEG, MEG, and ECoG data. APERTURE allows flexible multivariate analysis of ERPs and oscillatory activity and supports mass-univariate analysis with advanced statistical tests. Computations are accelerated using parallel computing supported through the MATLAB distributed computing toolbox. Examination of large, high-dimensional datasets is made simple through data visualization tools, including advanced plotting routines and generation of PDF reports with many figures.
Proper citation: APERTURE (RRID:SCR_014082) Copy
https://github.com/esctrionsit/snphub
Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data.
Proper citation: SnpHub (RRID:SCR_018177) Copy
https://discourse.data-against-covid.org/t/list-of-pis-supporting-this-endeavour/124
Group of volunteer data scientists, machines learning experts, bioinformaticians and professional software developers who have joined together to offer their expertise for any data analysis problems that arise in context of ongoing coronavirus pandemic.
Proper citation: Data-Against-COVID Team (RRID:SCR_018288) Copy
https://www.mbfbioscience.com/biolucida
Enables visualization, storage and sharing of large image data. Cloud based system by MBF Bioscience to help with data from 2D and 3D slide scanners, confocal Z-stacks, lightsheet whole brain images. System for data storage and management, data analysis and visualization. Data is stored in secure and permanent way. Available also is free application named Biolucida Viewer, for viewing public images or images shared by collaborators owning Biolucida.
Proper citation: Biolucida (RRID:SCR_018256) Copy
https://www.flidea.tech/flic-support
R Code used to analyze FLIC data. Functions are provided to examine interactions with food for single well and food choice experiments when fly makes physical contact with liquid food.
Proper citation: R scripts for FLIC data analysis (RRID:SCR_018386) Copy
https://cole-trapnell-lab.github.io/monocle3/
Software analysis toolkit for single cell RNA-seq. Used for single cell RNA-Seq experiments. Unsupervised algorithm that increases temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points.
Proper citation: Monocle3 (RRID:SCR_018685) Copy
http://dambe.bio.uottawa.ca/DAMBE/dambe.aspx
Software package for data analysis in molecular biology and evolution. Integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data. Used for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers.
Proper citation: DAMBE (RRID:SCR_018528) Copy
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