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http://weizhong-lab.ucsd.edu/metagenomic-analysis/
A customizable web server for fast metagenomic analysis.
Proper citation: WebMGA (RRID:SCR_011951) Copy
An ELN (electronic lab notebook) software application where researchers can record and organize their data by recording, dragging, and dropping elements. Users can utilize tools and features such as image annotation, search and filter, protocol templates, and team communication. The format of the ELN is customizable and can be rearranged at any point.
Proper citation: labfolder (RRID:SCR_013974) Copy
A web-based application designed with an easy-to-use interface to facilitate the high-throughput assessment and prioritization of genes and missense alterations important for cancer tumorigenesis.
Proper citation: CRAVAT (RRID:SCR_012776) Copy
A web server designed to provide a total solution to analyze small RNAs sequencing data generated by SOLEXA., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: DSAP (RRID:SCR_013352) Copy
http://www.csie.ntu.edu.tw/~cjlin/libsvm
An integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM) from the laboratory of Chih-Chung Chang and Chih-Jen Lin. It supports multi-class classification.
Proper citation: LIBSVM (RRID:SCR_010243) Copy
http://thenode.biologists.com/
The Node: a community site for development biologists
Proper citation: The Node (RRID:SCR_013071) Copy
Commercial organizations which develops, manufactures, and sells solutions and equipment for blood sampling, blood gas analysis, transcutaneous monitoring, and IT management systems under certain brand names.
Proper citation: Radiometer (RRID:SCR_014772) Copy
https://sift.bii.a-star.edu.sg/sift4g/AboutSIFT4G.html
Software tool to predict whether amino acid substitution affects protein function. Faster version of SIFT that enables to scale up and provide SIFT predictions for more organisms.
Proper citation: SIFT 4G (RRID:SCR_021850) Copy
Manufacturer and supplier of the DMZ Universal electrode pullers which produce pipettes and electrodes with a tip diameter down to 0.2 micrometers.
Proper citation: Zeitz (RRID:SCR_014774) Copy
Artificial intelligence image analysis platform that facilitates life science research. It offers data analysis, processing functions, and security features to accelerate research productivity.
Proper citation: IMACEL (RRID:SCR_015868) Copy
http://www.detaibio.com/sms2/protein_gravy.html
Web protein hydrophilicity analysis tool.
Proper citation: protein hydrophilicity analysis tool (RRID:SCR_023015) Copy
https://docs.google.com/presentation/d/13KqqDOFLbhCPRsCqf4zETdcjhZECIXD_/edit#slide=id.p1
MJFF in partnership with Aligning Science Across Parkinson’s are in the process of establishing data platform, CRN Cloud, leveraging Verily Workbench to share data generated by researcher labs funded through ASAP Collaborative Research Network. The data types include mainly raw and processed single cell RNA-seq, single nucleus RNA-seq, and bulk RNA-seq from both PD and healthy control samples.
Proper citation: Collaborative Research Network Cloud (RRID:SCR_023923) Copy
https://git.integromics.fr/published/predomics
Software package for metagenomics data. Discovers accurate predictive signatures and provides unprecedented interpretability. Package contains three methods for suppervised learning based on ternary coefficients. Used to discover classification models for quantitative metagenomics data.
Proper citation: Predomics (RRID:SCR_017415) Copy
http://www.people.fas.harvard.edu/~junliu/em/em.htm
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A haplotype inference program.
Proper citation: EM-DECODER (RRID:SCR_000023) Copy
https://github.com/wilsonGW/SomaDetection
Source code for a machine learning method to detect somas on confocal microscopic images of the Drosophila brain. The method can be applied to the original raw images where the noises are not removed and the number of somas is unknown.
Proper citation: SomaDetection (RRID:SCR_015717) Copy
http://viewer.shigen.info/cgi-bin/crispr/crispr.cgi
Web tool to show micro homology sequences striding over double strand break point created by CRISPR/Cas9 system. Used to search for CRISPR target site with micro-homology sequences. Used to predict deletion pattern.
Proper citation: NBRP Medaka CRISPR target site (RRID:SCR_018159) Copy
http://nucleobytes.com/index.php/4peaks
Software application for viewing and editing sequence trace files.
Proper citation: 4Peaks (RRID:SCR_000015) Copy
Gene atlas of Type 2 Diabetes Mellitus associated complex disorders. Provides curated and integrated information about genes involved in development and progression of Type 2 Diabetes Mellitus, genes and pathways with evidence for role in diabetes under risk factors including obesity, diet, inflammation, stress and complex disorders that are associated with Type 2 Diabetes Mellitus including atherosclerosis, diabetic retinopathy, diabetic nephropathy, diabetic neuropathy, cardiovascular disease.
Proper citation: T2DiACoD (RRID:SCR_019092) Copy
https://mzmatch.sourceforge.net/MetAssign.php
Software that combines information from the mass-to-charge ratio, retention time and intensity of each peak, together with a model of the inter-peak dependency structure, to increase the accuracy of peak annotation. The software has been implemented as part of the mzMatch metabolomics analysis pipeline, which is available for download.
Proper citation: MetAssign (RRID:SCR_000092) Copy
Software tool as catalog of inferred sequence binding preferences. Online library of transcription factors and their DNA binding motifs.
Proper citation: CIS-BP (RRID:SCR_017236) Copy
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