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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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25 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]
Intended Audience : Developers [Filter]
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Intended Audience : Other Audience [Filter]
License : OSI Approved : BSD License [Filter]
Natural Language : English (Now Filtering)
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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. 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 (Now Filtering) 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

2. 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 (Now Filtering)
Natural Language : German [Filter]
Operating System : Microsoft : Windows [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

3. 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]
Intended Audience : End Users/Desktop [Filter]
License : OSI Approved : GNU General Public License (GPL) [Filter]
Natural Language : English (Now Filtering)
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Programming Language : Fortran [Filter]
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Topic : Biostatistics & Medical Statistics [Filter]
Topic : Genetics [Filter]
Topic : Multivariate Statistics : Linear Models [Filter]

Activity Percentile: 0.00

Registered: 2011-11-10 03:57

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

Development Status : 5 - Production/Stable [Filter]
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Programming Language : R (Now Filtering)
Topic : Bioinformatics : Visualization [Filter]
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Topic : High Performance Computing [Filter]

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Registered: 2019-07-16 15:34

5. genoPlotR - plot gene and genome maps - genoPlotR is a R package to produce reproducible, publication-grade graphics of gene and genome maps. It allows the user to read from usual format such as protein table files and blast results, as well as home-made tabular files.

Development Status : 5 - Production/Stable [Filter]
Environment : Console (Text Based) [Filter]
Environment : X11 Applications [Filter]
Intended Audience : Developers [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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Topic : Bioinformatics : Visualization [Filter]
Topic : Genetics [Filter]

Activity Percentile: 0.00

Registered: 2010-01-08 16:59

6. 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 (Now Filtering) 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

7. 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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License : OSI Approved : GNU General Public License (GPL) [Filter]
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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

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]
Intended Audience : Developers [Filter]
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License : OSI Approved : GNU General Public License (GPL) [Filter]
Natural Language : English (Now Filtering)
Natural Language : French [Filter]
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Activity Percentile: 0.00

Registered: 2008-07-28 09:03

9. RFLPtools - RFLPtools provides functions to analyse DNA fragment samples (i.e. derived from RFLP-analysis) and standalone BLAST report files (i.e. DNA sequence analysis).

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

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Registered: 2010-02-24 09:24

10. 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]
License : OSI Approved : GNU Lesser General Public License (LGPL) [Filter]
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Registered: 2013-04-11 08:27

11. 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 (Now Filtering) 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

12. umx: A helper library for SEM in OpenMx - umx provides functions making it easy to build, run, modify, and report the results of Structural Equation Models (SEM) using OpenMx. Examples include setting start values: umxStart(); labels: umxLabel(); and reporting; umxSummary().

Development Status : 4 - Beta [Filter]
Environment : Console (Text Based) [Filter]
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License : OSI Approved : Artistic License [Filter]
Natural Language : English (Now Filtering)
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Operating System : POSIX : BSD [Filter]
Programming Language : R (Now Filtering)
Topic : Genetics [Filter]
Topic : Multivariate Statistics [Filter]
Topic : Optimization : General Purpose Continuous Solvers [Filter]

Activity Percentile: 0.00

Registered: 2013-08-28 13:52

13. 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

14. 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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Topic : Bioinformatics : Medical Science [Filter]
Topic : Genetics [Filter]

Activity Percentile: 0.00

Registered: 2011-03-23 10:20

15. 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 (Now Filtering) 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

16. 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]
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Registered: 2010-01-08 10:31

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

Development Status : 4 - Beta [Filter]
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Registered: 2013-05-29 18:34

18. 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]
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Registered: 2009-05-19 20:01

19. Priority Index - Priority Index or PI accelerates target selection through networking genetic evidence.

Development Status : 3 - Alpha [Filter]
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Registered: 2016-04-21 23:06

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