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https://github.com/llawas/Rice_HxD_Recovery_Metabolomics
Software tool as source code used in analysis of GC MS data from rice samples. Workflow for statistical analysis of GC MS data from field grown rice collected during rewatering after exposure to combined drought and heat stress.
Proper citation: Rice_HxD_Recovery_Metabolomics (RRID:SCR_017204) Copy
Software for 3D reconstruction from serial slices. Used to create 3D model to analyse organs, tissues and cells, create photos and videos to help scientists in life science, biology and medicine, visualize, analyze and exploit information from serial slices and get accurate quantitative information from reconstructed 3D models.
Proper citation: BioViz3D (RRID:SCR_017162) Copy
https://www.cbrg.ox.ac.uk/cbrg/
Core provides bioinformatics training and analysis tools. Supports bioinformatics analysis at University of Oxford.
Proper citation: University of Oxford Computational Biology Research Group Core Facility (RRID:SCR_017166) Copy
https://www.plantsci.cam.ac.uk/bioinformatics
Core provides assistance in data analysis to support members of Plant Sciences.
Proper citation: University of Cambridge Department of Plant Sciences Bioinformatics Core Facility (RRID:SCR_017164) Copy
https://github.com/dodomorandi/hatspil
Software Python tool for high throughput sequencing analysis, focused on high reliability, modularity and customisability.
Proper citation: HaTSPiL (RRID:SCR_017059) Copy
https://bioportainer.github.io/BioPortainer/
Open source software designed in modular way, aimed at facilitating user interaction with Docker environments in three different computational layers like infrastructure, platform and application.
Proper citation: BioPortainer (RRID:SCR_017058) Copy
Software R package for calculating, applying, evaluating and plotting results of polygenic risk scores analysis. Performs simulation study to estimate P value significance threshold for high resolution PRS studies and produces plots for inspection of results. Operating Unix/Linux.
Proper citation: PRSice (RRID:SCR_017057) Copy
https://labs.gladstone.org/bioinformatics/index.html
Core provides consulting services, sequencing, data analysis, and programming assistance. Used for Experimental Design and Power Analysis Consultation, RNA-seq, ChIP-seq, ATAC-seq analysis, Statistics consulting, Variant calling, Data normalization across multiple projects, General programming, Custom Figures for publication, tutorials for learning common software tools.
Proper citation: UCSF Gladstone Institutes Bioinformatics Core Facility (RRID:SCR_017178) Copy
https://www.bmh.manchester.ac.uk/research/facilities/bioinformatics/
Core provides assistance in integrative analysis of genomic datasets to support faculty.
Proper citation: University of Manchester Bioinformatics Core Facility (RRID:SCR_017171) Copy
https://www.ie-freiburg.mpg.de/
Interdisciplinary research institute that conducts basic research in modern immunobiology, developmental biology and epigenetics.
Proper citation: Max Planck Institiute of Immunobiology and Epigenetics; Freiburg; Germany (RRID:SCR_017170) Copy
Core at Vall dHebron Institut de Recerca, Barcelona, Spain to provide data analysis, softwares and training programs in statistics and bioinformatics for clinical research at VHIR.
Proper citation: Vall dHebron Institut de Recerca Statistics and Bioinformatics Unit Core Facility (RRID:SCR_017175) Copy
https://github.com/Frederik-D-Weber/cosleep
Software Python tool for sleep EEG analysis. Used for Closed and Open loop in Slow Ocillations, Sleep Stimulation in Auditory or Recording in full PSG using OpenBCI Cyton.
Proper citation: COsleep (RRID:SCR_017053) Copy
https://genome.duke.edu/cores-and-services/genomic-analysis-and-bioinformatics
Genomic Analysis and Bioinformatics core for data analysis associated with performing complex and data intensive projects in life science research of Duke University and Duke Medical School. Provides expertise, training, data analysis in next generation sequencing, array and proteomic based technologies.
Proper citation: Duke University Omics Data Analysis Core Facility (RRID:SCR_017174) Copy
https://github.com/macmanes-lab/BinPacker/blob/master/README
Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux.
Proper citation: BinPacker (RRID:SCR_017038) Copy
https://github.com/INTABiotechMJ/MITE-Tracker
Open source software tool for identifying miniature inverted repeat transposable elements in large genomes. Used to process large scale genomes, to find and classify MITEs using an efficient alignment strategy to retrieve nearby inverted repeat sequences.
Proper citation: MITE-Tracker (RRID:SCR_017030) Copy
Core provides consultation, training, software and educational tools in bioinformatics and graphics.
Proper citation: Whitehead Institute Bioinformatics and Research Computing Core Facility (RRID:SCR_017150) Copy
https://github.com/g2-bernotas/PS-Plant-Framework
Software tool as end to end software for data acquisition, processing, and result extraction of Arabidopsis thaliana growth. Framework uses photometric stereo based 3D imaging system with computer vision and deep learning for tracking and quantifying both plant growth and movement parameters.
Proper citation: PS-Plant Framework (RRID:SCR_017032) Copy
https://ous-research.no/bioinformatics/
Core facility provides high throughput sequencing data analysis, metagenomics data analysis, proteomics data analysis, protein structure analysis, functional genomics, programming, scripting, and database or web services.
Proper citation: Rikshospitalet-Radiumhospitalet and University of Oslo Bioinformatics Core Facility (RRID:SCR_017152) Copy
https://github.com/BDI-pathogens/phyloscanner
Software tool for analysing pathogen genetic diversity and relationships between and within hosts at once, in windows along genome. Inferring transmission from within and between host pathogen genetic diversity.
Proper citation: phyloscanner (RRID:SCR_017400) Copy
Commercial organization located in Abingdon, United Kingdom for high technology products. Manufactures instruments for agriculture, astronomy, automotive, aerospace, bio-imaging, life science, chemical and catalysis, energy generation and storage, forensics, environmental industries, geology, metallurgy, pharmacy, photonics, polymers, quantum technology, data storage, and microelectronics. Products are divided into atom force microscopy, electron microscopy, deposition and etch tools, low temperature systems, optical imaging, nuclear magnetic resonance, MRI and CT servicing, Modular optical spectroscopy, and X-Ray.
Proper citation: Oxford Instruments (RRID:SCR_017366) Copy
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