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https://t1dexchange.org/research/biobank/

Collection of biological samples linked to participant medical data from individuals living with type 1 diabetes. Unifies samples and data from eight different clinical studies related to type 1 diabetes.

Proper citation: T1D Exchange Biobank (RRID:SCR_017195) Copy   

•   Source: SciCrunch Registry

https://github.com/llawas/Rice_HxD_Metabolomics

Source code used in the analysis of GC MS data from rice samples. Workflow for statistical analysis of GC MS data from field grown rice exposed to combined drought and heat stress.

Proper citation: Source code for analysis of GC-MS data - Rice HxD Project (RRID:SCR_017073) Copy   

•   Source: SciCrunch Registry

https://github.com/Inria-Visages/Anima-Scripts-Public

Open source scripts for medical image processing. Provides set of scripts in Python shell. These scripts use essentially tools from Anima to perform more complex series like image preprocessing, model estimation, atlas creation.

Proper citation: Anima scripts (RRID:SCR_017072) Copy   

•   Source: SciCrunch Registry

https://github.com/josephryan/matemaker

Software tool to make artificial mate pairs from long sequences for scaffolding.

Proper citation: matemaker (RRID:SCR_017199) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/RNAmmer/

Software package to predict ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models. Consistent and rapid annotation of ribosomal RNA genes.

Proper citation: RNAmmer (RRID:SCR_017075) Copy   

•   Source: SciCrunch Registry

https://github.com/nolanlab/VORTEX

Software Java graphical tool for single cell analysis, clustering and visualization. Provides multithreaded implementations of clustering algorithms, including nonparametric density based X shift, Hierarchical clustering, Mean shift and K medoids.

Proper citation: VORTEX (RRID:SCR_017047) Copy   

•   Source: SciCrunch Registry

https://github.com/greenhouselab/Veta

Software suite of functions for EMG data visualization and processing. Open source Matlab toolbox for electromyography combined with transcranial magnetic stimulation. MATLAB toolbox for the collection, analysis, and visualization of EMG and TMS.

Proper citation: VETA (RRID:SCR_017201) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.biovis3d.com/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://prsice.info/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://en.vhir.org/portal1/article_menu_serveis.asp?s=serveis&contenttypeid=43&contentid=1250&t=Presentation

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry