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Cloud-based high performance computing for specialised analyses on environmental omics.
Proper citation: Cloud-SPAN (RRID:SCR_025594) Copy
https://appyters.maayanlab.cloud/#/hTFtarget_Harmonizome_ETL
Comprehensive database for regulations of Human Transcription Factors and their targets. Provides tools for visualization, interpretation, and analysis of pathway knowledge.
Proper citation: hTFtarget (RRID:SCR_025626) Copy
https://tristanic.github.io/isolde/
Software environment to ease task of building macromolecular models into low to medium resolution experimental maps. Physically realistic environment for model building into low-resolution electron-density maps. Can generate maps directly from crystallographic F/sigF data in MTZ format and automatically re-calculate them when model changes, and/or generate "static" maps from pre-calculated F/phi data.
Proper citation: ISOLDE (RRID:SCR_025577) Copy
https://camarades.shinyapps.io/ASySD/
Open source, interoperable software tool to remove duplicate citations in biomedical systematic reviews.
Proper citation: Automated Systematic Search Deduplicator (RRID:SCR_025607) Copy
Portal built for the release and sharing of data resources of "Big Earth Data Science Engineering Program (CASEarth)" launched by the Chinese Academy of Sciences. A global raster data of land cover and land use. This data can be used for mapping and spatial modeling in Geographic Information Systems (GIS) or other computer programs. This website is not accessible from the USA.
Proper citation: Chinese CASEarth Data Sharing and Service Portal (RRID:SCR_025660) Copy
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
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