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Topic > Genetics

Linkage, LD and Haplotype Mapping (8 project)
Multiple Testing (4 project)
Phylogenetics (20 project)
Population Genetics (12 project)
QTL Mapping (3 project)

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26 projects in result set. Displaying 20 per page. Projects sorted by activity ranking.
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0. Benchmarking genomic data integration - Comparison pipeline for multi-platform data integration algorithms for functional genomics studies. Provides tools to compare performance between publicly available implementations

Development Status : 4 - Beta [Filter]
Development Status : 5 - Production/Stable [Filter]
Environment : Console (Text Based) [Filter]
Environment : X11 Applications [Filter]
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License : OSI Approved : BSD License [Filter]
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Programming Language : R (Now Filtering)
Topic : Bioinformatics [Filter]
Topic : Genetics [Filter]
Topic : Multivariate Statistics [Filter]

Activity Percentile: 0.00

Registered: 2011-02-02 00:51

1. RNetLogo (Discontinued) - RNetLogo is an interface to the agent-based modelling plattform NetLogo. NL can be embedded into the R environment with headless (no GUI) and interactive GUI mode. It provides functions to load models, execute commands and to get values from reporters.

Development Status : 5 - Production/Stable [Filter]
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License : OSI Approved : GNU General Public License (GPL) [Filter]
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Programming Language : Java [Filter]
Programming Language : R (Now Filtering)
Topic : Bioinformatics [Filter]
Topic : Genetics [Filter]
Topic : Social Sciences [Filter]

Activity Percentile: 0.00

Registered: 2011-08-19 15:59

2. Genotype Database Framework - GT.DB is a database framework for efficiently managing genome-wide genotype datasets (i.e. 10^6 or more biallelic markers, 1000s of samples), as well as underlying raw data and complex phenotype data, tightly integrated with R libraries for analysis.

Development Status : 4 - Beta [Filter]
Environment : Other Environment [Filter]
Intended Audience : Developers [Filter]
License : OSI Approved : GNU General Public License (GPL) [Filter]
Natural Language : English [Filter]
Operating System : OS Independent [Filter]
Programming Language : C/C\+\+ [Filter]
Programming Language : Other [Filter]
Programming Language : R (Now Filtering)
Topic : Bioinformatics [Filter]
Topic : Database [Filter]
Topic : Genetics [Filter]

Activity Percentile: 0.00

Registered: 2009-09-17 00:13

3. CellMix - Resources for performing gene expression deconvolution in R, i.e. estimating cell proportions and/or cell-specific gene expression from global gene expression measured in heterogeneous samples. Currently hosted packages: csSAM and CellMix packages.

Intended Audience : Developers [Filter]
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License : OSI Approved : GNU General Public License (GPL) [Filter]
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Programming Language : R (Now Filtering)
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Topic : Genetics [Filter]
Topic : Software Development [Filter]

Activity Percentile: 0.00

Registered: 2013-04-11 08:27

4. Low Rank Gaussian Process Regression - Fit a Low Rank Gaussian Process Regression / Linear Mixed Model for large datasets. These models are widely used in statistical genetics as a test of association while correcting for the confounding effects of kinship and population structure.
Environment : Console (Text Based) [Filter] License : OSI Approved : GNU General Public License (GPL) [Filter] Natural Language : English [Filter] Operating System : MacOS [Filter] Operating System : POSIX : Linux [Filter] Programming Language : C/C\+\+ [Filter] Programming Language : R (Now Filtering) Topic : Bioinformatics : Statistics [Filter] Topic : Genetics [Filter]	Activity Percentile: 0.00 Registered: 2013-12-19 15:12

5. LazyMLVA - This project automates assignment of MLVA (Multiple locus VNTR (Variable-Number-of-Tandem-Repeats) Analysis) types from files straight out of the sequencer.
Development Status : 2 - Pre-Alpha [Filter] Environment : Console (Text Based) [Filter] Intended Audience : End Users/Desktop [Filter] License : OSI Approved : GNU General Public License (GPL) [Filter] Natural Language : English [Filter] Operating System : OS Independent [Filter] Programming Language : R (Now Filtering) Topic : Bioinformatics [Filter] Topic : Genetics [Filter]	Activity Percentile: 0.00 Registered: 2010-01-08 10:31

6. synbreed - Collection of statistical and genetic methods developed for the synbreed project for synergistic plant and animal breeding.

Development Status : 4 - Beta [Filter]
Intended Audience : Developers [Filter]
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License : OSI Approved : GNU General Public License (GPL) [Filter]
Natural Language : English [Filter]
Natural Language : German [Filter]
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Programming Language : R (Now Filtering)
Topic : Bioinformatics : Statistics [Filter]
Topic : Bioinformatics : Visualization [Filter]
Topic : Genetics [Filter]

Activity Percentile: 0.00

Registered: 2010-03-05 10:51

7. Illumina Methylation Analyzer - This IMA package provided a pipeline to analyze Illumina’s 450k Infinium Methylation data. We aimed to find the differential methylated CpG island on user-customized annotated regions as well as individual site by using different methods.
Development Status : 2 - Pre-Alpha [Filter] Intended Audience : End Users/Desktop [Filter] License : OSI Approved : GNU General Public License (GPL) [Filter] Natural Language : English [Filter] Operating System : POSIX : Linux [Filter] Programming Language : R (Now Filtering) Topic : Bioinformatics [Filter] Topic : Genetics [Filter]	Activity Percentile: 0.00 Registered: 2011-08-17 20:46

8. SeqinR: Biological Sequences in R - The seqinR package for the R environment contains utilities to retrieve and analyse biological sequences.

Development Status : 5 - Production/Stable [Filter]
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License : OSI Approved : GNU General Public License (GPL) [Filter]
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Natural Language : French [Filter]
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Programming Language : R (Now Filtering)
Topic : Bioinformatics [Filter]
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Topic : Genetics [Filter]

Activity Percentile: 0.00

Registered: 2008-07-28 09:03

9. Non-Additive Inverses - A package to construct Non-Additive Genetic relatedness matrices and their generalized inverses for inclusion in quantitative genetic analyses using the 'animal model'.

Development Status : 5 - Production/Stable [Filter]
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License : OSI Approved : GNU General Public License (GPL) [Filter]
Natural Language : English [Filter]
Operating System : OS Independent [Filter]
Programming Language : Fortran [Filter]
Programming Language : R (Now Filtering)
Topic : Biostatistics & Medical Statistics [Filter]
Topic : Genetics [Filter]
Topic : Multivariate Statistics : Linear Models [Filter]

Activity Percentile: 0.00

Registered: 2011-11-10 03:57

10. CNVScope - CNVScope: Visually exploring copy number aberrations in cancer genomes

Development Status : 5 - Production/Stable [Filter]
Environment : Console (Text Based) [Filter]
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Topic : Bioinformatics : Visualization [Filter]
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Topic : High Performance Computing [Filter]

Activity Percentile: 0.00

Registered: 2019-07-16 15:34

11. casper - casper infers alternative splicing from high-throughput sequencing data both for known variants and de novo discovery. We use a Bayesian model with few assumptions, and modern model selection ideas with improved theoretical and computational properties.

Development Status : 4 - Beta [Filter]
Environment : Console (Text Based) [Filter]
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License : OSI Approved : GNU General Public License (GPL) [Filter]
Natural Language : English [Filter]
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Programming Language : R (Now Filtering)
Topic : Bayesian Statistics [Filter]
Topic : Bioinformatics : Statistics [Filter]
Topic : Genetics [Filter]

Activity Percentile: 0.00

Registered: 2011-10-11 08:51

12. Genome-wide analysis using MOSS - Performs genome-wide analysis of dense SNP array data using the mode oriented stochastic search (MOSS) algorithm in a case-control design. Includes preprocessing of the data from Plink format to the format required by the MOSS algorithm.

Development Status : 3 - Alpha [Filter]
Environment : Console (Text Based) [Filter]
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Natural Language : English [Filter]
Operating System : POSIX : Linux [Filter]
Programming Language : C/C\+\+ [Filter]
Programming Language : Fortran [Filter]
Programming Language : R (Now Filtering)
Topic : Bayesian Statistics [Filter]
Topic : Genetics [Filter]
Topic : Graphical Models [Filter]

Activity Percentile: 0.00

Registered: 2011-01-07 17:53

13. aroma.* packages [MOVED TO GITHUB] - This repository and all of its packages have been moved to https://github.com/HenrikBengtsson/

Development Status : 3 - Alpha [Filter]
Development Status : 4 - Beta [Filter]
Development Status : 5 - Production/Stable [Filter]
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Programming Language : R (Now Filtering)
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Registered: 2009-05-19 20:01

14. Sublogo dendrograms - Sublogo dendrograms are statistical graphics that reveal correlation in biological sequence alignments.

Development Status : 5 - Production/Stable [Filter]
Environment : Console (Text Based) [Filter]
Environment : Web Environment [Filter]
Intended Audience : Developers [Filter]
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License : OSI Approved : GNU General Public License (GPL) [Filter]
Natural Language : English [Filter]
Operating System : POSIX : Linux [Filter]
Programming Language : PHP [Filter]
Programming Language : R (Now Filtering)
Programming Language : Unix Shell [Filter]
Topic : Bioinformatics : Visualization [Filter]
Topic : Genetics [Filter]
Topic : Graphics : Plotting [Filter]

Registered: 2009-06-19 09:14

15. cgen - Parallel Genomic Prediction and GWAS in R using Eigen and Rcpp

Development Status : 4 - Beta [Filter]
Environment : Console (Text Based) [Filter]
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License : OSI Approved : GNU General Public License (GPL) [Filter]
Natural Language : English [Filter]
Natural Language : German [Filter]
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Registered: 2013-05-29 18:34

16. MELON - Methylation Enriched LOci Normalization for genome-wide DNA methylation experiments
Development Status : 3 - Alpha [Filter] Intended Audience : Developers [Filter] Intended Audience : End Users/Desktop [Filter] Programming Language : R (Now Filtering) Topic : Bioinformatics [Filter] Topic : Biostatistics & Medical Statistics [Filter] Topic : Genetics [Filter]	Activity Percentile: 0.00 Registered: 2012-04-18 14:21

17. GWAtoolbox - An R-package implemented for genome-wide association studies. The main feature is very vast quality check of data before meta-analysis. It provides an extensive list of quality statistics presented using easy-to-use DHTML and graphical outputs.

Development Status : 5 - Production/Stable [Filter]
Environment : Console (Text Based) [Filter]
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License : OSI Approved : GNU General Public License (GPL) [Filter]
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Operating System : MacOS [Filter]
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Programming Language : R (Now Filtering)
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Registered: 2011-03-23 10:20

18. plantbreeding - plantbreeding: R Software package for analysis and visualization of data from plant breeding and genetics experiments.
Development Status : 4 - Beta [Filter] License : OSI Approved : GNU General Public License (GPL) [Filter] Natural Language : English [Filter] Operating System : Microsoft : Windows [Filter] Programming Language : R (Now Filtering) Topic : Bioinformatics : Statistics [Filter] Topic : Design of Experiments & Analysis of Experimental Data [Filter] Topic : Genetics [Filter]	Activity Percentile: 0.00 Registered: 2012-07-01 21:32

19. Statistical analysis of DNA mixtures - Statistical analysis of mixed traces of DNA with artefacts. Features include parameter-fitting, visual diagnostics, evaluation of the likelihood, and genotype prediction. Full functionality requires a licenced copy of Hugin (www.hugin.com).
Development Status : 4 - Beta [Filter] Intended Audience : Developers [Filter] Intended Audience : End Users/Desktop [Filter] License : OSI Approved : GNU General Public License (GPL) [Filter] Natural Language : English [Filter] Operating System : OS Independent [Filter] Programming Language : R (Now Filtering) Topic : Genetics [Filter] Topic : Graphical Models [Filter]	Activity Percentile: 0.00 Registered: 2013-07-07 18:26

26 projects in result set. Displaying 20 per page. Projects sorted by activity ranking.
<1>