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https://github.com/jenniferfranks/FSQN
Software R package to perform feature specific quantile normalization. Designed to quantile normalize each feature in data set according to its corresponding feature in target distribution. This eliminates distribution based differences resulting from the use of different gene expression profiling platforms.
Proper citation: Feature Specific Quantile Normalization (RRID:SCR_025783) Copy
Funding organization for neurodegenerative disorders and use of AI in it. 501(c)(3) philanthropic initiative that seeks to accelerate the use of artificial intelligence (AI) in the fight against neurodegenerative diseases.
Proper citation: 10,000 Brains Project (RRID:SCR_025785) Copy
Software multi-modality post-processing suite for SPECT, CT, PET, MR, Optical and and Autoradiography imaging data.
Proper citation: Invicro Vivoquant (RRID:SCR_025778) Copy
https://github.com/EGA-archive/EuCanImage-FHIR
Software application as ETL implementation for EuCanImage, encouraging semantic interoperability of clinical data obtained in studies by transforming it into machine-readable format following FHIR standards. This parser uses FHIR Resources in order to create dictionaries following FHIR compliant structure. Code Language is written in Python 3.11. Outputs are JSON files compliant with FHIR 4.3 schemas.This script is specifically created for the Extract, Transform and Load implementation for EuCanImage, and will follow the structures obtained from the REDCap databases within the study.
Proper citation: EuCanImage FHIR ETL Implementation (RRID:SCR_025824) Copy
https://CRAN.R-project.org/package=ssMutPA
Software R tool designed for single-sample mutation-based pathway analysis by integrating somatic mutation data with protein-protein interaction (PPI) networks.
Proper citation: Single-sample Mutation-based Pathway Analysis (RRID:SCR_025644) Copy
https://seer.cancer.gov/seerstat/
Statistical software for analysis of SEER and other cancer-related databases.Used to view individual cancer records and to produce statistics for studying impact of cancer on population.
Proper citation: SEER*Stat (RRID:SCR_025808) Copy
Software developed by Bruker for analysis and processing of spectroscopic data. Used for measurement, processing and evaluation of IR, NIR and Raman spectra.
Proper citation: Bruker OPUS (RRID:SCR_025806) Copy
https://4nsi.com/scanning-services/
Industrial x-ray facilities with microfocus and high energy 2D and CT systems. Provides instruments for biological CT scanning as service.
Proper citation: North Star Imaging US Labs (RRID:SCR_025754) Copy
https://github.com/ElemeFE/element-angular
Open-source angularjs theme. Element for Angular.
Proper citation: ElemeFE element-angular (RRID:SCR_025725) Copy
https://pubmed.ncbi.nlm.nih.gov/36123081/
Behavior change intervention software. Participants enter their data as part of online survey, and software generates individualized feedback letters.
Proper citation: PAL:Proactive Automatized Lifestyle intervention (RRID:SCR_025727) Copy
https://github.com/HKU-BAL/Clair3
Software tool as germline small variant caller for long-reads. Symphonizing pileup and full-alignment for high-performance long-read variant calling.
Proper citation: Clair3 (RRID:SCR_026063) Copy
https://github.com/rwnull/insitu_probe_generator?tab=readme-ov-file
Code generated for use in Python to create DNA probes for use in hybridisation chain reaction, which allows for spatial resolution of mRNA expression with fluorescently tagged hairpins that bind to DNA probes. Used to generate HCR-style Probe Pairs for mRNA visualization.
Proper citation: rwnull / insitu_probe_generator (RRID:SCR_025981) Copy
https://github.com/Kizielins/q2-predict-dysbiosis/tree/master
Function-based gut microbiome health index.
Proper citation: q2-predict-dysbiosis (RRID:SCR_026038) Copy
https://pythonvideoannotator.readthedocs.io/en/master/index.html
Software graphical application written in Python, to analyze videos and create notes for events in the video. Used to identify animals’ behaviors based on information extracted from video.
Proper citation: PythonVideoAnnotator (RRID:SCR_025868) Copy
Portal showcases, aggregates, and facilitates the visualisation of non-human eukaryotic genome assemblies and genome annotations for species studied by Swedish research community, aiming to foster collaboration, highlight researchers’ work, and promote open science and FAIR data sharing.
Proper citation: Swedish Reference Genome Portal (RRID:SCR_026008) Copy
https://github.com/mysql/mysql-server
Open source Relational Database Management System that enables users to store, manage, and retrieve structured data efficiently.
Proper citation: MySQL-server (RRID:SCR_025972) Copy
https://github.com/STAR-Fusion/STAR-Fusion
Software tool to leverage chimeric and discordant read alignments identified by STAR aligner to predict fusions. Component of Trinity Cancer Transcriptome Analysis Toolkit. Used to identify candidate fusion transcripts supported by Illumina reads. Maps junction reads and spanning reads to reference annotation set.
Proper citation: STAR-Fusion (RRID:SCR_025853) Copy
https://www.wuxiapptec.com/services/
Pharmaceutical, biopharmaceutical, and medical device company founded in December 2000 in Shanghai. Contract research organization.
Proper citation: Wuxi AppTec (RRID:SCR_026235) Copy
https://github.com/lens-biophotonics/ZetaStitcher
Software tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.
Proper citation: ZetaStitcher (RRID:SCR_026193) Copy
https://github.com/di-0579/spatial_tri-omics
Software repository to share the raw data processing and visualization codes used in the spatial tri-omics project.
Proper citation: spatial_tri-omics (RRID:SCR_026194) Copy
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