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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

http://kim.bio.upenn.edu/software/pivot.shtml

Software R package for interactive analysis and visualization of transcriptomics data. Operating systems are macOS, Linux, Windows.

Proper citation: PIVOT software (RRID:SCR_017210) 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://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

https://github.com/cwatson/braingraph/

Software R package for performing graph theory analyses of brain MRI data.

Proper citation: brainGraph (RRID:SCR_017260) Copy   

•   Source: SciCrunch Registry

https://deeptools.readthedocs.io/en/develop/

Python based tools to process, visualize and analyse high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Implemented within Galaxy framework. Used to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches.

Proper citation: Deeptools (RRID:SCR_016366) Copy   

•   Source: SciCrunch Registry

https://github.com/sblanck/smagexp

Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more.

Proper citation: SMAGEXP (RRID:SCR_016360) Copy   

•   Source: SciCrunch Registry

https://github.com/mikessh/migec

Software package for analysis of immune repertoire sequencing data. Used for recovery of T Cell Receptor ( TCR ) data from bulk population data.Used for high-throughput sequencing data analysis. Allows for error correction while preserving the natural diversity of complex immune repertoires.

Proper citation: migec (RRID:SCR_016337) Copy   

•   Source: SciCrunch Registry

http://www.flir.jp/instruments/display/?id=54865

Software application for thermography for FLIR Systems. It has a basic thermal image analysis function including color palette and image adjustment function. Used to analyse the thermographic measurement data.

Proper citation: FLIR tools (RRID:SCR_016330) Copy   

•   Source: SciCrunch Registry

https://hub.docker.com/r/biodepot/star-for-criu/

Software as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability.

Proper citation: star-for-criu (RRID:SCR_016294) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/mica/

Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging.

Proper citation: masked ICA (mICA) Toolbox (RRID:SCR_016349) Copy   

•   Source: SciCrunch Registry

https://lifebit.ai/

Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines.

Proper citation: Lifebit Deploit (RRID:SCR_016428) Copy   

•   Source: SciCrunch Registry

https://www.denovosoftware.com/?gclid=EAIaIQobChMI36rn3-Dd3AIV2ud3Ch27lw2oEAAYASAAEgLbRvD_BwE

Software tool for flow and image cytometry data analysis by De Novo Software company.

Proper citation: FCS Express (RRID:SCR_016431) Copy   

•   Source: SciCrunch Registry

https://sleepdata.org/datasets/shhs

Portal for a multi-cohort study focused on sleep-disordered breathing and cardiovascular outcomes implemented by the National Heart Lung and Blood Institute. Recorded signals are: EEG, ECG, EOG, SaO2, HR, EOG, EMG, respiratory inductance plethysmography, respiration (thermistor), position, light.

Proper citation: Sleep Heart Health Study (RRID:SCR_016559) Copy   

•   Source: SciCrunch Registry

https://github.com/xu-lab/SINCERA

Software tool implemented in R S4 as an analytic pipeline for processing single-cell RNA-seq data from a whole organ or sorted cells. Used for Single Cell RNA-Seq profiling analysis.

Proper citation: SINCERA Pipeline (RRID:SCR_016563) Copy   

•   Source: SciCrunch Registry

http://mib.helsinki.fi/

Software package for advanced image processing, analysis, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets.

Proper citation: Microscopy Image Browser (RRID:SCR_016560) Copy   

•   Source: SciCrunch Registry

https://github.com/mpi2/vpv

Software tool as a desktop 3D volume viewer. Used for analysing results of automatic phenotype detection from the LAMA pipeline. Developed in Python using QT, and the PyQtGraph.

Proper citation: VPV (RRID:SCR_016545) Copy   

•   Source: SciCrunch Registry

https://cm.jefferson.edu/rna22/

Software tool as a pattern based algorithm for detecting microRNA binding sites and their corresponding microRNA and mRNA complexes. Allows interactive exploration and visualization of miRNA target predictions. Permits link-out to external expression repositories and databases.

Proper citation: RNA22 (RRID:SCR_016507) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/00-0210

Scanner for microarray analysis to scan next-generation higher-density arrays, including SNP arrays, tiling arrays for transcription and all-exon arrays for whole-genome analysis.

Proper citation: GeneChip™ Scanner 3000 7G (RRID:SCR_016522) Copy   

•   Source: SciCrunch Registry

https://www.uamh.ca/

Repository of microbial in Canada. Culture collection, preservation, analysis, identification of fungi living strains. Backed up by herbarium dried colonies. A reference and training centre for the identification of human and animal pathogens and allied taxa.Provides advice or assistance to projects involving fungi.

Proper citation: UAMH Centre for Global Microfungal Biodiversity (RRID:SCR_016466) Copy   

•   Source: SciCrunch Registry