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http://bioinf.wehi.edu.au/software/elda/
Software tool for limiting dilution analysis, with particular attention to needs of stem cell assays. Provides confidence intervals for all LDA data sets, including those with 0% or 100% responses. Other features include test of adequacy of single hit hypothesis, tests for frequency differences between multiple data sets, and ability to take advantage of cases where number of cells in sample is counted exactly.
Proper citation: ELDA (RRID:SCR_018933) Copy
https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/
Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR.
Proper citation: PROCHECK (RRID:SCR_019043) Copy
https://cran.r-project.org/web/packages/igraph/
Software package for graphs and network analysis. Provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.Can be programmed in R, Python, Mathematica, C/C Plus Plus.
Proper citation: igraph (RRID:SCR_019225) Copy
Web platform for electronic data capture by OpenClinica, LLC. Used as clinical trial management system.
Proper citation: OpenClinica (RRID:SCR_019223) Copy
http://www.bio-rad.com/en-eh/product/cfx-manager-software
Software tool to analyze real-time PCR data and run PCR system in software controlled mode., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CFX Manager (RRID:SCR_017251) Copy
http://rna.urmc.rochester.edu/RNAstructureWeb/Servers/Predict1/Predict1.html
Web server for RNA and DNA secondary structure prediction and analysis. Software package as RNA folding prediction program.
Proper citation: RNAstructure (RRID:SCR_017216) Copy
http://clustalw.ddbj.nig.ac.jp/index.php
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.Web sevice of ClustalW provided by DNA data bank of Japan.
Proper citation: ClustalW (RRID:SCR_017277) Copy
http://www.biosoft.com/w/calcusyn.htm
Software tool for drug mixtures study and establishing efficacy. Dose effect analyzer of combined drugs. Able to quantify synergism and inhibition. CalcuSyn Version 2.0 has Undo and Redo tools.
Proper citation: CalcuSyn (RRID:SCR_020251) 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://www.iconplc.com/innovation/nonmem/
Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions.
Proper citation: NONMEM (RRID:SCR_016986) Copy
https://www.denovosoftware.com/?gclid=EAIaIQobChMI36rn3-Dd3AIV2ud3Ch27lw2oEAAYASAAEgLbRvD_BwE
Software tool for flow and image cytometry data analysis by De Novo Software company.
Proper citation: FCS Express (RRID:SCR_016431) Copy
https://www.ncbi.nlm.nih.gov/Web/Newsltr/Spring04/blastlab.html
Software tool as a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. Used to make non redundant sequence sets.
Proper citation: BLASTClust (RRID:SCR_016641) Copy
http://grigoriefflab.janelia.org/ctffind4
Software tool for finding CTFs of electron micrographs. Program used for the estimation of objective lens defocus parameters from transmission electron micrographs. The program CTFFIND3 is an updated version of the program CTFFIND2. For micrographs collected on photographic film and scanned in use CTFFIND 3. For images from CCDs or direct detectors use CTFFIND 4.
Proper citation: CTFFIND (RRID:SCR_016732) Copy
https://blake.bcm.edu/emanwiki/EMAN2
Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography.
Proper citation: EMAN (RRID:SCR_016867) Copy
Software package for sequence alignment, assembly and analysis. Integrated and extendable desktop software platform for organization and analysis of sequence data. Bioinformatics software platform packed with molecular biology and sequence analysis tools.
Proper citation: Geneious (RRID:SCR_010519) Copy
http://www.moleculardevices.com/Products/Software/GenePix-Pro.html
Industry standard microarray image analysis software because of its unique combination of imaging and analysis tools, visualizations, automation capabilities, performance and intuitive workflows.
Proper citation: GenePix Pro (RRID:SCR_010969) Copy
http://www.illumina.com/software/genomestudio_software.ilmn
Visualize and analyze data generated by all of Illumina''s platforms.
Proper citation: GenomeStudio (RRID:SCR_010973) Copy
http://www.bu.edu/jlab/wp-assets/ComBat/Abstract.html
Adjusting batch effects in microarray expression data using Empirical Bayes methods.
Proper citation: ComBat (RRID:SCR_010974) Copy
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