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https://github.com/magnusmanske/snpomatic

Short read mapping software. Read mapping tool offering variety of analytical output functions, with emphasis on genotyping,

Proper citation: snpomatic (RRID:SCR_024348) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/harvardinformatics/NGmerge

Software tool for merging paired-end reads via novel empirically derived models of sequencing errors. Used for merging paired-end reads and removing adapters. Corrects errors and ambiguous bases and assigns quality scores for merged bases that accurately reflect the error rates.

Proper citation: NGmerge (RRID:SCR_024483) Copy   

•   Source: SciCrunch Registry

http://www.workrave.org/

Software tool to assist in recovery and prevention of Repetitive Strain Injury. Monitors keyboard and mouse usage and using this information, it frequently alerts you to take microbreaks, rest breaks and restricts you to your daily computer usage.

Proper citation: Workrave (RRID:SCR_024364) Copy   

•   Source: SciCrunch Registry

http://xmedcon.sourceforge.net/

Open source software toolkit for medical image conversion.

Proper citation: XMedCon (RRID:SCR_024366) Copy   

•   Source: SciCrunch Registry

http://www.ks.uiuc.edu/Research/vmd/

Software tool as molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.

Proper citation: VMD (RRID:SCR_024368) Copy   

•   Source: SciCrunch Registry

https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/dna-amplicon.html

Local Run Manager DNA Amplicon analysis module aligns amplicon reads against reference specified in the manifest file. Variants are called for the targeted regions.

Proper citation: DNA Amplicon (RRID:SCR_024481) Copy   

•   Source: SciCrunch Registry

https://github.com/miRTop/mirtop

Command lines tool to annotate miRNAs with standard mirna/isomir naming.

Proper citation: mirtop (RRID:SCR_024116) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/mpsqed/

Software tool for the design of multiplex pyrosequencing assays.

Proper citation: mPSQed (RRID:SCR_024118) Copy   

•   Source: SciCrunch Registry

http://www-igm.univ-mlv.fr/~marsan/smile_english.html

Software tool that infers motifs in set of sequences to infer exceptionnal sites as binding sites in DNA sequences. 1.4 version allows to infer motifs written on any alphabet in any kind of sequences. Allows to deal with motifs associated by some distance constraints. Used to group under unique model different occurrences composed of several boxes separated by spacers of different lengths.

Proper citation: SMILE (RRID:SCR_024119) Copy   

•   Source: SciCrunch Registry

https://www.pkdcure.org/

Organization and funder of polycystic kidney disease research to find treatments. The organization also raises awareness for the disease through education, advocacy and support.

Proper citation: PKD Foundation (RRID:SCR_000209) Copy   

•   Source: SciCrunch Registry

http://research.mssm.edu/cnic/tools-rayburst.html

A software application which provides the source code for the Rayburst Algorithm. The fully automated algorithm casts rays in a 2D/3D dataset without the use of pre-generated ray tables. It is implemented in ANSI C as a single module. The most current version is Version 1.1, last updated on Aug. 15, 2006.

Proper citation: Rayburst Open-Source Code (RRID:SCR_013799) 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://wpicr.wpic.pitt.edu/WPICCompGen/fdr/

Software application (entry from Genetic Analysis Software)

Proper citation: WEIGHTED FDR (RRID:SCR_013442) 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://www7.inra.fr/mia/T/MendelSoft/

Software application for identifying all Mendelian inconsistencies in complex pedigree data with thousand of individuals, including many loops and several errors. Can also infer missing genotypes. (entry from Genetic Analysis Software)

Proper citation: MENDELSOFT (RRID:SCR_013177) Copy   

•   Source: SciCrunch Registry

http://hadoop.apache.org/

Software library providing a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models. It is designed to scale up from single servers to thousands of machines, each offering local computation and storage. Rather than rely on hardware to deliver high-availability, the library itself is designed to detect and handle failures at the application layer, so delivering a highly-available service on top of a cluster of computers, each of which may be prone to failures. The project includes these modules: * Hadoop Common: The common utilities that support the other Hadoop modules. * Hadoop Distributed File System (HDFS): A distributed file system that provides high-throughput access to application data. * Hadoop YARN: A framework for job scheduling and cluster resource management. * Hadoop MapReduce: A YARN-based system for parallel processing of large data sets.

Proper citation: Apache Hadoop (RRID:SCR_011879) 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