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http://www.prisma-statement.org/

Evidence based minimum set of items for reporting in systematic reviews and meta analyses. Focuses on reporting of reviews evaluating randomized trials, but can also be used as basis for reporting systematic reviews of other types of research, particularly evaluations of interventions.

Proper citation: PRISMA (RRID:SCR_018721) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://autodock.scripps.edu/

Software suite of automated docking tools. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure. AutoDock consist of AutoDock 4 and AutoDock Vina. AutoDock 4 consists of autodock to perform docking of ligand to set of grids describing target protein, and autogrid to pre calculate these grids.

Proper citation: AutoDock (RRID:SCR_012746) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html

Software package that includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements.

Proper citation: ChIPpeakAnno (RRID:SCR_012828) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/minfi.html

Software tools for analyzing and visualizing Illumina''s 450k array data.

Proper citation: minfi (RRID:SCR_012830) Copy   

•   Source: SciCrunch Registry

http://repeatmasker.org/

Software tool that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher. RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library ) and RepBase ( consensus sequence library ).

Proper citation: RepeatMasker (RRID:SCR_012954) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/affy.html

Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis.

Proper citation: affy (RRID:SCR_012835) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://ccb.jhu.edu/software/tophat/index.shtml

Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.

Proper citation: TopHat (RRID:SCR_013035) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.openclinica.com/

Web platform for electronic data capture by OpenClinica, LLC. Used as clinical trial management system.

Proper citation: OpenClinica (RRID:SCR_019223) Copy   

•   Source: SciCrunch Registry

http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss

A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.

Proper citation: Trans-ABySS (RRID:SCR_013322) Copy   

•   Source: SciCrunch Registry

http://www.eisenlab.org/eisen/?page_id=42

Software to graphically browse results of clustering and other analyses from Cluster.

Proper citation: TreeView (RRID:SCR_013503) Copy   

•   Source: SciCrunch Registry

https://automeris.io/WebPlotDigitizer/

Web based tool to extract data from plots, images, and maps. HTML5 based online tool to extract numerical data from plot images. Used to reverse engineer images of data visualizations to extract underlying numerical data.

Proper citation: WebPlotDigitizer (RRID:SCR_013996) Copy   

•   Source: SciCrunch Registry

http://www.malvern.com/en/products/technology/nanoparticle-tracking-analysis/

Software which utilizes the properties of both light scattering and Brownian motion to obtain the particle size distribution of samples in liquid suspension. The Nanoparticle Tracking Analysis software tracks many particles individually and calculates their hydrodynamic diameters using the Stokes Einstein equation.

Proper citation: Nanoparticle Tracking Analysis (RRID:SCR_014239) Copy   

•   Source: SciCrunch Registry

http://www.jmp.com/en_us/software/jmp.html

Statistical software that uses dynamic graphics rather than tables or graphs to visualize raw data. More specific versions of JMP are available for statistical analyses, clinical work, and genomics. Features include statistical modeling, data cleanup, automation and scripting, and experimental design.

Proper citation: JMP (RRID:SCR_014242) Copy   

•   Source: SciCrunch Registry

https://www.phenix-online.org/documentation/reference/phaser.html

Crystallographic software which solves structures using algorithms and automated rapid search calculations to perform molecular replacement and experimental phasing methods.

Proper citation: Phaser (RRID:SCR_014219) Copy   

•   Source: SciCrunch Registry

http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/

Software for macromolecular model building, model completion and validation, and protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, rigid-body fitting, ligand search, Ramachandran plots, non-crystallographic symmetry and more. Source code is available.

Proper citation: Coot (RRID:SCR_014222) Copy   

•   Source: SciCrunch Registry

http://molprobity.biochem.duke.edu

A structure-validation web application which provides an expert-system consultation about the accuracy of a macromolecular structure model, diagnosing local problems and enabling their correction. MolProbity works best as an active validation tool (used as soon as a model is available and during each rebuild/refine loop) and when used for protein and RNA crystal structures, but it may also work well for DNA, ligands and NMR ensembles. It produces coordinates, graphics, and numerical evaluations that integrate with either manual or automated use in systems such as PHENIX, KiNG, or Coot.

Proper citation: MolProbity (RRID:SCR_014226) Copy   

•   Source: SciCrunch Registry

http://www.waters.com/waters/en_US/MassLynx-MS-Software/nav.htm?cid=513662&locale=en_US

Software which can acquire, analyze, manage, and share mass spectrometry data. MassLynx controls any Waters mass spectrometry system, from sample and solvent management components to mass spectrometer and auxiliary detectors. The software can acquire nominal mass, exact mass, MS/MS and exact mass MS/MS data. The software system also maintains and consolidates all user sample data. Optional Application Manager programs provide additional information for specific MS analyses and data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MassLynx (RRID:SCR_014271) Copy   

•   Source: SciCrunch Registry