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http://cmpg.unibe.ch/software/BayeScan/index.html
Software tool to identify candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.
Proper citation: BayeScan (RRID:SCR_022018) Copy
https://github.com/deeptools/HiCExplorer
Software tool to analyse Hi-C and capture Hi-C data. Command line suite of tools to process, normalize and visualize Hi-C data.
Proper citation: HiCExplorer (RRID:SCR_022111) Copy
https://www.mirion.com/products/genie-2000-basic-spectroscopy-software
Software tool as comprehensive environment for data acquisition, display and analysis of gamma and alpha spectrometry data.
Proper citation: Genie 2000 Basic (RRID:SCR_021933) Copy
https://github.com/Murali-group/SARS-CoV-2-network-analysis
Software tool to predict human proteins that interact with SARS-CoV-2 proteins and trace provenance of predictions.
Proper citation: SARS-CoV-2 network analysis (RRID:SCR_021811) Copy
https://www.ibm.com/products/spss-statistics
Software package for statistics. Used to analyze and visualize data. Extensions can be used, Python and R programming language code, to integrate with open source software. Available for Windows and Mac operating systems.Versions that were produced by SPSS Inc. before the IBM acquisition (Versions 18 and earlier) would be given origin or publisher of SPSS Inc. in Chicago. Versions that were released after the acquisition would be given origin or publisher of IBM Corp. in Armonk, NY.
Proper citation: IBM SPSS Statistics (RRID:SCR_016479) Copy
https://www.mayo.edu/research/labs/tissue-repair-mechanobiology/software
Software tool to calculate 2D tractions exerted by adherent cell on its substrate. Used in field of mechanobiology to study contractile responses of variety of cell types.
Proper citation: TractionsForAll (RRID:SCR_021819) Copy
https://github.com/VisionandCognition/NHP-pycortex
Software tool as adaptation for NHP brains and pipelines. Pycortex python based toolkit for surface visualization of fMRI data.
Proper citation: NHP pycortex (RRID:SCR_021815) Copy
https://github.com/jtamames/SqueezeMeta
Software tool as fully automated pipeline for metagenomic analysis. Used for metagenomics covering all steps of analysis. Features several characteristics including co-assembly procedure or co-assembly of unlimited number of metagenomes via merging of individual assembled metagenomes, both with read mapping for estimation of abundances of genes in each metagenome. Includes binning and bin checking for retrieving individual genomes.
Proper citation: SqueezeMeta (RRID:SCR_021821) Copy
http://computproteomics.bmb.sdu.dk:8192/app/PolySTest
Web service for statistical testing, data browsing and interactive visualization. Contains multiple statistical tests and new method to incorporate missing values. Robust statistical testing of proteomics data with missing values to improve detection of biologically relevant features., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: PolySTest (RRID:SCR_021942) Copy
https://bioconductor.org/packages/BASiCS/
Software tool for Bayesian analysis of single cell sequencing data. Used to perform statistical analyses of single cell RNA sequencing datasets in context of supervised experiments.
Proper citation: Bayesian Analysis of Single Cell Sequencing (RRID:SCR_021829) Copy
Software tool used to plot circular plots and visualize genomic data along genomic locations.
Proper citation: Circa (RRID:SCR_021828) Copy
Collaboration between research institutes working to provide framework of regulatory genomic elements in individuals with neuropsychiatric disorders.Collaboration has resulted in comprehensive set of manuscripts published in Science providing new insights into biology of developing, adult, and diseased human brain.Manuscripts are organized around three flagship articles, first analyzing human development, second studying disease transcriptomes, and third integrating tissue and single cell data with deep learning approaches.
Proper citation: PsychENCODE (RRID:SCR_021760) Copy
http://combo.dbe.unifi.it/medusa
Web server of multi draft based scaffolder.Exploits information obtained from set of genomes from related organisms to determine correct order and orientation of contigs.
Proper citation: MeDuSa (RRID:SCR_022058) Copy
Improved model quality assessments using Rosetta energy terms. Predictor combines training features from ProQRosCen, ProQRosFA and ProQ2.
Proper citation: ProQ3 (RRID:SCR_021880) Copy
Public research university in Golden, Colorado, founded in 1874. School offers both undergraduate and graduate degrees in engineering, science, and mathematics, with focus on energy and environment.
Proper citation: Colorado School of Mines; Golden; Colorado (RRID:SCR_022054) Copy
https://prosa.services.came.sbg.ac.at/prosa.php
Interactive web service for recognition of errors in three dimensional structures of proteins.
Proper citation: ProSA web (RRID:SCR_021879) Copy
https://www.zeiss.com/microscopy/int/products/microscope-software/labscope.html
Software tool for image acquisition using WiFi-enabled Zeiss microscopes. Compatible with Windows PCs and with Apple tablets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Zeiss LabScope (RRID:SCR_021768) Copy
https://www.ionoptix.com/products/software/ionwizard-core-and-analysis/
Software tool to perform rapid fluorescence and morphometric real time, synchronous data acquisition with IonOptix systems, as well as polynomial fitting and analysis for myocyte research. Features include data trace averaging and filtering,composite images, and transient analysis. Integrates presentation of fluorescence traces and images, analog voltages, and cell length data under intuitive interface. Analyzes raw data by performing ratio, ion, or linear calibration calculations.
Proper citation: IonWizard (RRID:SCR_021764) Copy
http://biomine.cs.vcu.edu/servers/MFDp2/
Web tool for accurate prediction of disorder in proteins by fusion of disorder probabilities, content and profiles.
Proper citation: MFDp2 (RRID:SCR_021885) Copy
https://prdos.hgc.jp/cgi-bin/top.cgi
Web server to predict natively disordered regions of protein chain from its amino acid sequence. Returns disorder probability of each residue as prediction results.
Proper citation: PrDOS (RRID:SCR_021886) Copy
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