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https://github.com/nighres/nighres
Software package for processing of high-resolution neuroimaging data. Nighres is a community-developed project that aims to make neuroscience data tools easier to install, use and extend.
Proper citation: Nighres (RRID:SCR_016287) Copy
https://github.com/Sung-Huan/ANNOgesic
Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data.
Proper citation: ANNOgesic (RRID:SCR_016326) Copy
http://www.nitrc.org/projects/longhippsegm/
Software based on robust registration and simultaneous hippocampal segmentation and longitudinal marker classification of brain MRI of an arbitrary number of time points. The framework comprises two parts: a longitudinal segmentation and a longitudinal classification step.
Proper citation: Longitudinal neuroimaging hippocampal markers for diagnosing Alzheimer's disease (RRID:SCR_016282) Copy
https://huttenhower.sph.harvard.edu/humann2
Software for profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data Used for millions of short DNA/RNA reads. This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members.
Proper citation: HUMAnN2 (RRID:SCR_016280) Copy
https://github.com/jbelyeu/SV-plaudit
Software for rapidly curating structural variant (SVs) predictions. SV-plaudit provides a pipeline for creating image views of genomic intervals, automatically storing them in the cloud, deploying a website to view/score them, and retrieving scores for analysis.
Proper citation: SV-plaudit (RRID:SCR_016285) Copy
https://sites.google.com/site/sigenproject/
Software to extract and trace neuronal structure from confocal laser scanning microscope images. It performs the automatic reconstruction of neurons for image stacks and can generate compartmental models of neurons as swc file format data.
Proper citation: SIGEN (RRID:SCR_016284) Copy
https://www.jax.org/jax-mice-and-services
Supplier of mice for research purposes.
Proper citation: JAX Mice and Services (RRID:SCR_016408) Copy
Global biotechnology company based in Shanghai, China, specializing in custom model organisms, humanized and immunodeficient mice, and gene-editing services for preclinical research. Alternatively, in molecular biology, it can refer to knockout or mutant mice lacking the Smoc1 or Smoc2 genes (secreted modular calcium-binding proteins) used to study embryonic, eye, and limb development.Supplier of mice for research purposes. Provides technical services, model organisms, gene editing and decoding.
Proper citation: Shanghai Model Organisms Center (RRID:SCR_016407) Copy
Supplier of mice for research purposes.
Proper citation: National Resource Center for Mutant Mice (RRID:SCR_016406) Copy
Supplier of mice for research purposes.
Proper citation: Taconic Biosciences (RRID:SCR_016410) Copy
https://bitbucket.org/mugqic/genpipes/src/master/
Software for genomics and bioinformatics analysis. GenPipes includes several python pipelines that cover many genomics applications, such as RNASeq, ChIPSeq, DNASeq, WGBS, HiC, Metagenomics, PacBio assembly, etc.
Proper citation: GenPipes (RRID:SCR_016376) Copy
https://www.genomics.agilent.com/article.jsp?pageId=2100
Software that performs data analysis algorithms for QPCR data. The software is included with the purchase of the Agilent MxPro QPCR System., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MxPro QPCR (RRID:SCR_016375) Copy
http://bioconductor.org/packages/release/bioc/html/MetaCyto.html
Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database.
Proper citation: MetaCyto (RRID:SCR_016415) Copy
Supplier of Frogs and Tadpoles for the scientific community.
Proper citation: Xenopus Express (RRID:SCR_016373) Copy
http://www.monicahealthcare.com/products/labour-and-delivery/monica-novii-wireless-patch-system
A peel and stick in-room ambulatory fetal monitoring solution by Monica Healthcare Ltd. Measures fetal heart rate (FHR), maternal heart rate (MHR) and uterine activity (UA).
Proper citation: Monica monitor (RRID:SCR_016416) Copy
Web page for cyclic immunofluorescence. It lists several downloadable data and software pertaining to cyclic immunofluorescence.
Proper citation: CycIF.org (RRID:SCR_016267) Copy
http://www.nitrc.org/projects/vdb/
Virtual resource for neuroscience.
Proper citation: Virtual Digital Brain (RRID:SCR_016265) Copy
Develops information technologies that make authoring complete metadata more manageable. Its products aim to facilitate using the metadata in further research.Center to improve metadata and its use throughout biomedical sciences. Develops information technologies that make authoring complete metadata more manageable through better interfaces, terminology, metadata practices, and analytics. Optimizes metadata pathway from provider to end user. Provides way for funders to specify what metadata they want to collect as part of research life cycle.
Proper citation: Center for Expanded Data Annotation and Retrieval (RRID:SCR_016269) Copy
https://www.phc.ox.ac.uk/research/technology-outputs/easygv
Software for calculating different measures of glycaemic variability (GV). It analyzes continuous glucose monitoring data using a simple interface.
Proper citation: easyGV (RRID:SCR_016260) Copy
https://www.illumina.com/systems/sequencing-platforms/miseqdx.html
MiSeqDx System is FDA-regulated, CE-IVD-marked, NGS platform for in vitro diagnostic (IVD) testing. System offers both diagnostic and research modes.
Proper citation: Illumina: MiSeqDx System (RRID:SCR_016380) Copy
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