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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://github.com/PyWavelets/pywt
Software Python package for wavelet analysis.
Proper citation: PyWavelets (RRID:SCR_024421) Copy
https://sciex.com/products/software/proteinpilot-software
Software tool for protein identification and protein expression analysis. Used to identify proteins and search large numbers of post translational modifications, without increasing search time or false positives. Compatible with all proteomics MS/MS systems.
Proper citation: ProteinPilot (RRID:SCR_024414) Copy
https://github.com/paulgeeleher/pRRophetic
Software R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. Used to predict phenotypes from gene expression microarray data, gene expression microarray data,
Proper citation: pRRophetic (RRID:SCR_024417) 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://www.miltenyibiotec.com/products/macs-flow-cytometry/software/flowlogic-software.html
Software tool for flow cytometry data analysis by Miltenyi Biotec.
Proper citation: Flowlogic (RRID:SCR_020942) Copy
Software tool used to create summary of findings tables for cochrane systematic reviews. Web application to create, manage and share summaries of research evidence called Evidence Profiles and Summary of Findings Tables.
Proper citation: GRADEpro (RRID:SCR_021308) Copy
https://pypi.org/project/jcvi/
Software tool as collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.
Proper citation: jcvi (RRID:SCR_021641) 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 major university
Proper citation: University of Texas at Austin; Texas; USA (RRID:SCR_005900) Copy
https://github.com/Illumina/strelka/
Software for somatic single nucleotide variant (SNV) and small indel detection from sequencing data of matched tumor-normal samples. Strelka2 germline and somatic small variant caller.
Proper citation: Strelka2 (RRID:SCR_005109) Copy
Software free desktop Windows application for the management and analysis of microbiology laboratory data with a particular focus on antimicrobial resistance surveillance developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance at the Brigham and Women's Hospital in Boston, Massachusetts. WHONET, available in 44 languages, supports local, national, regional, and global surveillance efforts in over 2,300 hospital, public health, animal health, and food laboratories in over 130 countries worldwide.
Proper citation: WHONET (RRID:SCR_024495) Copy
https://www.certara.com/software/phoenix-pkpd/
Software to automate repetitive analysis steps and is widely considered the industry standard for NCA, TK, and PK/PD modeling. Used as non-compartmental analysis (NCA), pharmacokinetic/pharmacodynamic (PK/PD), and toxicokinetic (TK) modeling tool.
Proper citation: WinNonlin (RRID:SCR_024504) Copy
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