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https://www.photometrics.com/products/ocular
Scientific image acquisition software. Software allows color and monochrome cameras to capture high quality images and videos from their microscope or lens system.
Proper citation: Ocular (RRID:SCR_024490) Copy
https://github.com/SharonLutz/Umediation
Software R package that examines the role of unmeasured confounding in mediation analysis allowing for normally distributed or Bernoulli distributed exposures, outcomes, mediators, measured confounders, and unmeasured confounders. Umediation also accommodates multiple measured confounders, multiple unmeasured confounders, and allows for mediator exposure interaction on the outcome. Enables to simulate unmeasured confounding in mediation analysis in order to see how the results of the mediation analysis would change in the presence of unmeasured confounding.
Proper citation: Umediation (RRID:SCR_024492) Copy
https://www.reading.ac.uk/bioinf/IntFOLD/
Web integrated protein structure and function prediction server. Integrated server for modelling protein structures and functions from amino acid sequences.
Proper citation: IntFOLD (RRID:SCR_024523) Copy
https://www.malvernpanalytical.com/en/products/product-range/omnisec/accessories/omnisec-software
Software for OMNISEC instrument control, data acquisition, analysis and reporting. Used for advanced analysis of proteins and polymers by GPC/SEC, and is specifically designed for control of OMNISEC RESOLVE and OMNISEC REVEAL.
Proper citation: OMNISEC (RRID:SCR_024485) Copy
http://pbil.univ-lyon1.fr/software/phyldog/
Software tool to simultaneously build gene and species trees when gene families have undergone duplications and losses. Can analyze thousands of gene families in dozens of genomes simultaneously.
Proper citation: PHYLDOG (RRID:SCR_024487) Copy
https://github.com/chaoszhang/A-pro
Software tool for species tree reconstruction from multi-copy gene family trees.Used for estimating unrooted species tree given set of unrooted gene trees and is statistically consistent under the multi-species coalescent model. ASTRAL-pro extends ASTRAL to allow multi-copy genes. ASTRAL-Pro 2, ultrafast and memory efficient version of ASTRAL-Pro that adopts placement based optimization algorithm for significantly better scalability without sacrificing accuracy.
Proper citation: ASTRAL-Pro (RRID:SCR_024520) Copy
Web based survival analysis tool tailored for medical research. Used to assess correlation between expression of all genes (mRNA, miRNA, protein) and survival in samples from tumor types including breast, ovarian, lung, gastric, colon cancer, AML, and myeloma.
Proper citation: Kaplan Meier Plotter (RRID:SCR_024521) Copy
Software tool for image acquisition.Supports ProgRes microscope cameras and delivers optimal image quality and reproducible results.Included with all of Jenoptik ProgRes microscope cameras.
Proper citation: ProgRes Capture Pro (RRID:SCR_024489) Copy
Web server as ultra fast approach for large scale protein structure similarity searching.The upload protein structure file should be in PDB format. Used for searching similar protein structures by aligning input structure with the whole PDB library.
Proper citation: MADOKA (RRID:SCR_024522) Copy
https://cab.spbu.ru/software/spades/
Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SPAdes (RRID:SCR_000131) Copy
A web analysis system and resource, which provides comprehensive information on piRNAs in the widely studied mammals. It compiles all the possible clusters of piRNAs and also depicts piRNAs along with the associated genomic elements like genes and repeats on a genome wide map. piRNABank mainly provides data onnamely Human, Mouse, Rat, Zebrafish, Platypus and a fruit fly, Drosophila.Search options have been designed to query and obtain useful data from this online resource. It also facilitates abstraction of sequences and structural features from piRNA data. piRNABank provides the following features: * Simple search * Search piRNA clusters * Search homologous piRNAs * piRNA visualization map * Analysis tools, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: piRNABank (RRID:SCR_007858) Copy
Resource for reuse, sharing and meta-analysis of expression profiling data. Database and set of tools for meta analysis, reuse and sharing of genomics data. Targeted at analysis of gene expression profiles. Users can search, access and visualize coexpression and differential expression results.
Proper citation: Gemma (RRID:SCR_008007) Copy
A horizontally and vertically structured database that pulls scientific and medical information and describes it consistently using the Ingenuity Ontology. The Knowledge Base pulls information from journals, public molecular content databases, and textbooks. Data is curated and and integrated into the Knowledge Base .
Proper citation: Ingenuity Pathways Knowledge Base (RRID:SCR_008117) Copy
http://www.mutationtaster.org/
Evaluates disease-causing potential of sequence alterations.
Proper citation: MutationTaster (RRID:SCR_010777) Copy
http://www.ebi.ac.uk/Tools/sss/wublast/
Tool to find regions of sequence similarity within selected protein databases quickly, with minimum loss of sensitivity.
Proper citation: WU-BLAST (RRID:SCR_011824) Copy
A commercial software tool for statistical analysis.
Proper citation: SyStat (RRID:SCR_010455) Copy
Powerful, accessible statistical tools for fast visualization and analysis of microarrays - expression arrays, miRNA, exon arrays and genomics copy number data.
Proper citation: GeneSpring GX (RRID:SCR_010972) Copy
http://www.perkinelmer.com/pages/020/cellularimaging/products/openlab.xhtml
A software package for performing 2D microscope image processing and integrating and controlling a diverse array of instrumentation in a laboratory environment. The software suite has four basic areas of operation acquisition, image presentation, and storage, analysis, and automation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Openlab (RRID:SCR_012158) Copy
http://bioinf.cs.ucl.ac.uk/downloads/MetaPSICOV/
Software tool for accurate prediction of contacts and long range hydrogen bonding in proteins.
Proper citation: MetaPSICOV (RRID:SCR_024517) Copy
http://www.mbfbioscience.com/stereo-investigator
Stereo Investigator system includes microscope, computer, and Stereo Investigator software. Software works with Brightfield, Multi-Channel Fluorescence, Confocal, and Structured Illumination Microscopes. System used to provide estimates of number, length, area, and volume of cells or biological structures in tissue specimen in areas of neuroscience including neurodegenerative diseases, neuropathy, memory, and behavior, pulmonary research, spinal cord research, and toxicology.
Proper citation: MBF BioScience: Stereo Investigator (RRID:SCR_002526) Copy
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