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https://www.ie-freiburg.mpg.de/bioinformaticsfac

Core provides assistance in primary analysis of sequencing data and other large scale biocomputing. For our internal users we host extensive web services, workflows and customized tools that help with data management, visualizations, standardized analyses and data sharing.

Proper citation: Max Planck Institiute of Immunobiology and Epigenetics Bioinformatics Core Facility (RRID:SCR_017160) Copy   

•   Source: SciCrunch Registry

https://www.beckman.it/flow-cytometry/research-flow-cytometers/cytoflex/software

Software program that controls instrument operation, data collection and analysis. Software for CytoFLEX Platform by Beckman Coulter.

Proper citation: CytExpert Software (RRID:SCR_017217) Copy   

•   Source: SciCrunch Registry

https://github.com/EpistasisLab/pennai

Open source software tool to leverage supervised machine learning techniques to analyze data. Can assist with tasks such as choosing appropriate models for data. Data science assistant for generating results from large and complex data problems.

Proper citation: PennAI (RRID:SCR_017215) Copy   

•   Source: SciCrunch Registry

https://www.medsci.ox.ac.uk/research/labtalk/labtalk

Core provides genomics training, as well as assistance in next generation sequencing analyses.

Proper citation: University of Oxford Medical Sciences Division Computational Genomics: Analysis and Training Core Facility (RRID:SCR_017173) Copy   

•   Source: SciCrunch Registry

https://ircm.qc.ca/en/technological-services/bioinformatics

Core to support scientists within and outside IRCM in analysis of biological and clinical data, in particular high throughput genomic data. Operating on collaborative basis and paid services. Provides assistance with Data analysis for RNA-Seq, ChIP-Seq, RIP-Seq, DNA methylation, DNA-Seq, targeted sequencing of rRNAs, microarrays, customized training courses.

Proper citation: Montreal Clinical Research Bioinformatics Core Facility (RRID:SCR_017176) Copy   

•   Source: SciCrunch Registry

https://biocore.crg.eu/wiki/Main_Page

Provides services of consultation and data analysis, with focus on Next Generation Sequencing and other high throughput experiments, software and database development, and training in basic and advanced bioinformatics techniques. Services provided for fee to support collaborative grant funded investigations.

Proper citation: Centre for Genome Regulation Bioinformatics Core Facility (RRID:SCR_017145) Copy   

•   Source: SciCrunch Registry

https://github.com/aldenleung/OMTools

Software package for optical mapping data processing, analysis and visualization. Used to handle and explore large scale optical mapping profiles.

Proper citation: OMTools (RRID:SCR_017143) Copy   

•   Source: SciCrunch Registry

http://cleversysinc.com/CleverSysInc/?csi_products=topscan-suite

Software suite as top view based behavior analysis system by CleverSys Inc. Uses animal body parts to provide behavior analysis results. Used in experiments with animal tracking task.

Proper citation: TopScan (RRID:SCR_017141) Copy   

•   Source: SciCrunch Registry

https://www.varian.com/

Manufacturer located in Palo Alto, California, USA, that has made developments in fields of radiotherapy, radiosurgery, X-ray tube technology, digital image detectors, cargo screening, and non-destructive testing. Varian technology and software for processing diagnostic X-ray images is being used in radiotherapy and analysis.

Proper citation: Varian Medical Systems, Inc. (RRID:SCR_017372) Copy   

•   Source: SciCrunch Registry

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger

Software tool as set of analysis pipelines that process chromium single cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis by 10xGenomics.

Proper citation: Cell Ranger (RRID:SCR_017344) Copy   

•   Source: SciCrunch Registry

http://snf-515788.vm.okeanos.grnet.gr/

Web tool for integrating human and mouse microRNAs in pathways.Pathway analysis web-server, providing statistics, while being able to accommodate advanced pipelines. Web server for assessment of miRNA regulatory roles and identification of controlled pathways. Supports all analyses for KEGG molecular pathways and Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio).DIANA miRPath v.2.0 includes investigating combinatorial effect of microRNAs in pathways.DIANA-miRPath v3.0 includes deciphering microRNA function with experimental support., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DIANA-mirPath (RRID:SCR_017354) Copy   

•   Source: SciCrunch Registry

http://pathwaynet.princeton.edu/

Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks.

Proper citation: PathwayNet (RRID:SCR_017353) Copy   

•   Source: SciCrunch Registry

http://relacs.sourceforge.net/

Software platform for closed loop data acquisition, online analysis, and stimulus generation specifically designed for, but not limited to, electrophysiological recordings.

Proper citation: Relacs (RRID:SCR_017280) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/vesselucida360

Software tool for visualization and automatic reconstruction of microvascular networks in 3D environment with built-in analysis tools by MBF Bioscience.

Proper citation: Vesselucida 360 (RRID:SCR_017320) Copy   

•   Source: SciCrunch Registry

http://trimal.cgenomics.org/

Software tool for automated removal of spurious sequences or poorly aligned regions from multiple sequence alignment. Software package for automated alignment trimming in large scale phylogenetic analyses.

Proper citation: trimAl (RRID:SCR_017334) Copy   

•   Source: SciCrunch Registry

https://arxiv.org/abs/1308.2012

Software tool for estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Used as general and assembly independent method for estimating genomic characteristics.

Proper citation: GCE (RRID:SCR_017332) Copy   

•   Source: SciCrunch Registry

https://www.cmrr.umn.edu/downloads/mrspa

Software package to post process MR spectroscopy data. Magnetic Resonance signal processing and analysis software. Runs under Matlab.

Proper citation: MRspa (RRID:SCR_017292) Copy   

•   Source: SciCrunch Registry

https://github.com/NHLBI-BCB/IKAP

Software tool for identifying K mAjor cell population groups in single-cell RNA-seq analysis. Algorithm identifying major cell groups that improves differentiating by tuning parameters for clustering. Using multiple datasets improves identification of major cell types and facilitates cell ontology curation.

Proper citation: IKAP (RRID:SCR_017417) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/Glimma.html

Software package for interactive graphics for gene expression analysis. Generates interactive visualisations for analysis of RNA-sequencing data.

Proper citation: Glimma (RRID:SCR_017389) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/tdtdecodingtoolbox/

Software Matlab toolbox for multivariate analysis of functional and structural MRI data. Software package for multivariate analyses of functional imaging data.

Proper citation: The Decoding Toolbox (RRID:SCR_017424) Copy   

•   Source: SciCrunch Registry