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http://www.nitrc.org/projects/dcm2nii/

A tool for converting images from the complicated formats used by scanner manufacturers (DICOM, PAR/REC) to the NIfTI format used by various scientific tools. dcm2nii works for all modalities (CT, MRI, PET, SPECT) and sequence types.

Proper citation: dcm2nii (RRID:SCR_014099) Copy   

•   Source: SciCrunch Registry

http://faculty.washington.edu/browning/presto/presto.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Software application that calculates individual inbreeding (F) and average relatedness (AR) coefficients. Additionally, users can compute useful parameters in population genetics such as: the number of ancestors explaining genetic variability; the genetic importance of the herds; F statistics from genealogical information. (entry from Genetic Analysis Software)

Proper citation: ENDOG (RRID:SCR_013289) Copy   

•   Source: SciCrunch Registry

http://iso2mesh.sourceforge.net/

A Matlab / Octave-based mesh generation toolbox designed for easy creation of high quality surface and tetrahedral meshes from 3D volumetric images. It contains a rich set of mesh processing scripts/programs, functioning independently or interfacing with external free meshing utilities. Iso2mesh toolbox can operate directly on 3D binary, segmented or gray-scale images, such as those from MRI or CT scans, making it particularly suitable for multi-modality medical imaging data analysis or multi-physics modeling.

Proper citation: iso2mesh (RRID:SCR_013202) Copy   

•   Source: SciCrunch Registry

http://www.openbioinformatics.org/gengen/

A suite of free software tools to facilitate the analysis of high-throughput genomics data sets. The package is currently a work-in-progress and infrequently updated.

Proper citation: GenGen (RRID:SCR_013447) Copy   

•   Source: SciCrunch Registry

http://www.silkscientific.com/graph-digitizer.htm

Digitizer software which can convert graph images to useful (x,y) data by turning a scanner into an automatic graph digitizer. UN‑SCAN‑IT works with most image formats (TIFF, JPG, BMP, GIF, etc.) from any scanner, digital camera, or other image source to digitize plots, instrumental output, published graphs, etc. Its features include: automatically digitizing strip chart and xy recorder output, digitizing graphs that are on different scales to compare results, comparing data with published graphs of other investigators, digitizing old plots and charts for comparison with new data, and re‑scaling and appending existing printed graphs.

Proper citation: UN-SCAN-IT Graph Digitizer Software (RRID:SCR_013725) Copy   

•   Source: SciCrunch Registry

http://spina.sourceforge.net

Software tool to deliver estimated structure parameters of endocrine feedback control systems in vivo from serum or plasma hormone levels. Used for evaluation of thyroid function. Allows for calculating thyroid maximum secretory capacity (GT or SPINA-GT) and sum activity of peripheral 5'-deiodinases (GD or SPINA-GD) from levels of TSH, (F)T4 and (F)T3 that have been determined once only (SPINA Thyr). Binaries are available for Mac OS, Mac OS X, Palm OS, Garnet OS and Windows. For other operating systems, including Linux, Solaris and BSD, SPINA Thyr is available as sourcecode. Building from source requires THINK Pascal (for Mac OS Classic), winsoft PocketStudio (for Palm OS / Garnet OS) or Lazarus/Free Pascal (for Mac OS X, Windows, Linux, BSD and Solaris). Special version of calculation engine is available for modern S implementation, e.g. R.

Proper citation: SPINA Thyr (RRID:SCR_014352) Copy   

•   Source: SciCrunch Registry

http://faculty.washington.edu/browning/beaglecall/beaglecall.html

Software package for simultaneous genotype calling and haplotype phasing for unrelated individuals. BEAGLECALL produces output posterior genotype probabilities and output phased haplotypes. BEAGLECALL generates extremely accurate genotype calls because it uses both allele signal intensity data and inter-marker correlation to call genotypes. BEAGLECALL is designed for use with high-density SNP arrays, and it uses the BEAGLE haplotype frequency model to model inter-marker correlation. (entry from Genetic Analysis Software)

Proper citation: BEAGLECALL (RRID:SCR_013301) Copy   

•   Source: SciCrunch Registry

http://dlin.web.unc.edu/software/spreg-2/

Software program for performing regression analysis of secondary phenotype data in case-control association studies. Secondary phenotypes are quantitative or qualitative traits other than the case-control status. Because the case-control sample is not a random sample of the general population, standard statistical analysis of secondary phenotype data can yield very misleading results. SPREG implements valid and efficient statistical methods. (entry from Genetic Analysis Software)

Proper citation: SPREG (RRID:SCR_013261) Copy   

•   Source: SciCrunch Registry

http://biomath.med.uth.gr

Software application for performing genome scan meta-analysis, a quantitative method to identify genetic regions (bins) with consistently increased linkage score across multiple genome scans, and for testing the heterogeneity of the results of each bin across scans. The program provides as an output the average of ranks and three heterogeneity statistics, as well as corresponding significance levels. (entry from Genetic Analysis Software)

Proper citation: HEGESMA (RRID:SCR_013304) Copy   

•   Source: SciCrunch Registry

http://www.pypop.org/

Open-source software pipeline for population genomics. Designed for processing genotype and allele data and running population genetic analyses, including conformity to Hardy-Weinberg expectations; tests for balancing or directional selection; estimates of haplotype frequencies and measures and tests of significance for linkage disequilibrium.

Proper citation: PyPop (RRID:SCR_013425) Copy   

•   Source: SciCrunch Registry

http://www.multifactordimensionalityreduction.org/

Software application that is a data mining strategy for detecting and characterizing nonlinear interactions among discrete attributes (e.g. SNPs, smoking, gender, etc.) that are predictive of a discrete outcome (e.g. case-control status). The MDR software combines attribute selection, attribute construction and classification with cross-validation to provide a powerful approach to modeling interactions. (entry from Genetic Analysis Software)

Proper citation: MDR (RRID:SCR_013427) Copy   

•   Source: SciCrunch Registry

http://lbm.ab.a.u-tokyo.ac.jp/~iwata/antmap/

Software application based on the Ant Colony Optimization to solve the special case of the traveling salesman problem of ordering markers when the number of loci is large. ANYMAP performs segregation test, linkage grouping and locus ordering, and constructs a linkage map rapidly. (entry from Genetic Analysis Software)

Proper citation: ANTMAP (RRID:SCR_013426) Copy   

•   Source: SciCrunch Registry

http://www.danielsoper.com/statcalc3/

A set of many statistics calculators, including a confidence interval calculator.

Proper citation: Statistics Calculator (RRID:SCR_013827) Copy   

•   Source: SciCrunch Registry

http://www.gridqtl.org.uk/

Publicly available Web-based application that can perform QTL mapping on a variety of population types. GridQTL will extend the functionality of QTLExpress by adding new and advanced approaches for modelling QTL analysis in simple and complex populations. These new methods will be available on a Grid system that will offer flexible workflow management, resource allocation, data persistence, detached execution of simulations and the scalability required for the increase in data volume, data sources and complexity required by the new models. (entry from Genetic Analysis Software)

Proper citation: GRIDQTL (RRID:SCR_013397) Copy   

•   Source: SciCrunch Registry

http://www.bio-rad.com/en-us/sku/soft-om-sw-opticon-monitor-software

Software which controls all operations in the experimental setup, data acquisition and monitoring, and data analysis stages of the Bio-Rad Opticon 2 system. In the experimental setup stage, setup and programming operations are accessed from the Master File window. The master file consists of a plate file, which specifies the parameters of the plate, and a protocol file, which specifies the experimental conditions. After a plate and a protocol setup have been created or selected, a run can be initiated, which begins the data acquisition and monitoring stage. Data collection can be monitored during the run by viewing a plot of fluorescence intensity vs. cycle number. In the data analysis stage, data can be analyzed using the Quantitation, Melting Curve, and/or Analysis windows. The window used depends on the type of data being collected.

Proper citation: Opticon Monitor Software (RRID:SCR_014241) Copy   

•   Source: SciCrunch Registry

http://writefullapp.com

A software application which provides feedback on writing, wording, and frequency of text by checking against databases of correct language. Users can highlight a chunk of text and use Writefull to see how often the specific text appears in different language databases. Writefull can also offer synonyms and suggestions for wording. Writefull is supported by numerous writing tools which include MS Word and Gmail.

Proper citation: Writefull (RRID:SCR_014006) Copy   

•   Source: SciCrunch Registry

http://www.klayout.de/

A GDS and OASIS file viewer editor that has file overlay and file creation capabilities. It features include: layer grouping, flexible rulers, image overlay, partial editing functions, and external library support.

Proper citation: KLayout (RRID:SCR_014644) Copy   

•   Source: SciCrunch Registry

https://zenodo.org/record/17651

Software for interfacing with Tucker-Davis System 3 hardware. It is a Python wrapper around Tucker-Davis Technologies ActiveX library. Along with standard operations, the software can conduct type conversions between analog and digital units, handle robust errors, and has a remote procedure call server that allows multiple processes and/or programs to communicate with the hardware across the same connection.

Proper citation: TDTPy (RRID:SCR_014520) Copy   

•   Source: SciCrunch Registry

http://www.cns.atr.jp/dni/en/downloads/brain-decoder-toolbox/

Software that performs ?decoding? of brain activity, by learning the difference between brain activity patterns among conditions and then classifying the brain activity based on the learning results. BDTB is a set of Matlab functions. BDTB is OS-independent.

Proper citation: Brain Decoder Toolbox (RRID:SCR_013150) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/4363991

Software that allows users to manually or automatically design custom primers and probes for gene quantitation and allelic discrimination (SNP) real-time PCR applications. It supports assays based on TaqMan and SYBR Green I dye chemistries.

Proper citation: Primer Express (RRID:SCR_014326) Copy   

•   Source: SciCrunch Registry