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https://anima.irisa.fr

Portal provides software library and python scripts for medical image processing. Open source set of software tools for medical image processing, medical image analysis, image registration, statistical analysis, quantitative MRI processing, image denoising and filtering, and segmentation developed by VISAGES/Empenn research team. Available as Github repository and compiled binaries for various OS including OSX, Fedora, Ubuntu, Windows.

Proper citation: Anima (RRID:SCR_017017) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/gage/

Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies.

Proper citation: GAGE (RRID:SCR_017067) Copy   

•   Source: SciCrunch Registry

https://www.scanco.ch/microct100.html

Micro Computed Tomography 100 scanner for 3D imaging of specimens in vitro supplied with software for scanning, 3D analysis, visualization, image management and data import and export by SCANCO Medical AG.

Proper citation: Scanco: Medical microCT 100 system (RRID:SCR_017119) Copy   

•   Source: SciCrunch Registry

https://team.inria.fr/empenn/

Project between Inria, Inserm, CNRS, and University of Rennes for biomedical image analysis for understanding neurological disease. Used to diagnose, monitor and deliver treatment for mental, neurological and substance use disorders by establishing multidisciplinary team between information sciences and medicine in medical imaging, neuroinformatics and population cohorts.

Proper citation: Empenn (RRID:SCR_017074) 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/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/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://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

http://bioconductor.org/packages/release/data/experiment/html/affydata.html

Software R package for analysis of Affymetrix Data. Contains samples data files of a large size.

Proper citation: affydata (RRID:SCR_016976) Copy   

•   Source: SciCrunch Registry

https://www.ccpn.ac.uk/v2-software/software/analysis

Software package for interactive NMR spectrum visualization, resonance assignment and data analysis. Graphical elements allow to enter information and to view status of data and library functions manipulate the CCPN data model objects to record the scientific information. Software is cross platform and works on Linux, Mac OSX, Windows and Unix.

Proper citation: CCPN Analysis (RRID:SCR_016984) Copy   

•   Source: SciCrunch Registry

http://www.althia.es/

A biomedical company in Spain focused on the development of new tools for diagnosis and personalized treatment of oncological diseases and precancerous. It has three areas of activity in permanent innovation: Assistance in Diagnosis / Prognosis in solid and hematological tumors, Translational Research covering the gap between basic and clinical research and advanced radiotherapy treatments based image-guided single dose (SD-IGRT). Their objectives are: * Provide an integrated tissue and tumor molecular phenotype analysis using the most advanced technologies in diagnosis, to guide the most appropriate treatment for each patient. * Discover and validate molecular patterns by molecular systems and platforms including pathology, to generate predictive algorithms through computational biology, evolution and determining the response of patients with a particular tumor profile. Althia has laboratories equipped with the most advanced equipment and technologies in Barcelona and Granada Genyo Center, with offices in Madrid.

Proper citation: Althia (RRID:SCR_003918) Copy   

•   Source: SciCrunch Registry

http://www.alacris.de/

Commercial organization that uses next generation sequencing technologies coupled with computational modeling of tumor and somatic tissues in order to identify individualized therapies for cancer patients. The company also uses these technologies to help pharmaceutical partners stratify patients for their clinical trials. Alacris has an exclusive worldwide commercial license for the computational modeling of tumors and somatic tissues using proprietary computational systems modeling technologies ModCell developed at the Max Planck Institute for Molecular Genetics (MPI-MG) in Berlin coupled with next generation sequencing and genotyping technology developed at Harvard Medical School in Boston. The company also is building up the first next generation sequencing center in Europe for clinical operations.

Proper citation: Alacris Theranostics (RRID:SCR_003953) Copy   

•   Source: SciCrunch Registry

http://psynova.com/

Commercial organization focused on the development and exploitation of novel biomarkers for psychiatric illnesses. They provide industrial and academic partners with comprehensive biomarker discovery services in commercial and collaborative projects. They operate in the field of psychiatric disorders and their products and services are designed to excel biomarker research. In 2010, Psynova Neurotech and its partner company Rules-Based-Medicine Inc (now MyriadRBM) conducted a beta launch of a blood test aiding in the diagnosis of schizophrenia (http://www.veripsych.com/). They are now refining the test and have shifted their focus to the development of new blood-based biomarker tests that aid in the diagnosis, prognosis and differential diagnosis of schizophrenia, bipolar disorder and major depression. They offer not only their pre-selceted Multiple Reaction Monitoring (MRM) and Multiplex Immunoassay products, but also custom build panels. If they are provided with a list of analyses to evaluate, they can produce an analytical panel according to individual needs utilizing either MRM or Multiplex Immunoassay technologies., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Psynova Neurotech (RRID:SCR_003959) Copy   

•   Source: SciCrunch Registry

http://www.genomedics.it/

A commercial company specialized in the field of clinical governance, research and clinical-epidemiological analysis and development of services and software applications for healthcare. Products and Services * Analysis and development software solutions, web, e-learning * Design and Implementation APP for Smartphone and Tablet (iOS, Android, Windows Phone) * Clinical Intelligence & Clinical Decision Support Systems (CDSS) * Data center services and Application Server Provider * Epidemiology, Surveillance and Health Promotion - Development of studies and epidemiological research

Proper citation: Genomedics (RRID:SCR_004103) Copy   

•   Source: SciCrunch Registry

http://www.sierrasensors.com/

In 2018 Bruker acquired Sierra Sensors GmbH, based in Hamburg, Germany. Sierra develops and manufactures innovative analytical biosensors based on Surface Plasmon Resonance (SPR) detection. Driven by patented technologies in the areas of SPR detection and microfluidic sample delivery, Sierra instruments are setting a new standard in high-throughput and high-performance label-free analysis.

Proper citation: Sierra Sensors (RRID:SCR_004062) Copy   

•   Source: SciCrunch Registry

http://www.biomol-informatics.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 12, 2021. Technology based company in Madrid that offers consulting services on Bioinformatics in areas of research, diagnostics and pharmaceutical industry.

Proper citation: Biomol-Informatics (RRID:SCR_004081) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/vanator-cvr/

A Perl pipeline utilising a large variety of common alignment, assembly and analysis tools to assess the metagenomic profiles of Illumina deep sequencing samples. The emphasis is on the discovery of novel viruses in clinical and environmental samples.

Proper citation: Vanator (RRID:SCR_004370) Copy   

•   Source: SciCrunch Registry

http://www.nematodes.org/

Nematode & Neglected Genomics (at) The Blaxter Lab is a nematode related portal including databases and services. Resources include genomic and transcriptomic databases for nematodes and other metazoan phyla and freely downloadable software tools for expressed sequence tag analysis, DNA barcode analysis and phylogenomics. Major categories include: * GenePool * 959 Nematode Genomes * Teaching * Research Projects * Bioinformatics Software Tools * Lab Personnel * Lab Wiki * Genomics Databases * NEMBASE4 * Tardigrada: Hypsibius dujardini * Earthworm: Lumbricus rubellus * MolluscDB * ArthropodDB * other Neglected Genomes

Proper citation: nematodes.org (RRID:SCR_003267) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/cancer/software/genepattern

A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.

Proper citation: GenePattern (RRID:SCR_003201) Copy   

•   Source: SciCrunch Registry