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 Topic > Genetics
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20 projects in result set.
0. SeqinR: Biological Sequences in R - The seqinR package for the R environment contains utilities to retrieve and analyse biological sequences.
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- Development Status : 5 - Production/Stable [Filter]
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- License : OSI Approved : GNU General Public License (GPL) (Now Filtering)
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Registered: 2008-07-28 09:03 |
1. 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.
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- Development Status : 4 - Beta [Filter]
- Environment : Other Environment [Filter]
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- Programming Language : R [Filter]
- Topic : Bioinformatics [Filter]
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- Topic : Genetics [Filter]
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Registered: 2009-09-17 00:13 |
2. 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.
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- Development Status : 2 - Pre-Alpha [Filter]
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- License : OSI Approved : GNU General Public License (GPL) (Now Filtering)
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- Programming Language : R [Filter]
- Topic : Bioinformatics [Filter]
- Topic : Genetics [Filter]
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Registered: 2011-08-17 20:46 |
3. 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.
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- Development Status : 4 - Beta [Filter]
- Environment : Console (Text Based) [Filter]
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- Natural Language : English [Filter]
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- Programming Language : C/C\+\+ [Filter]
- Programming Language : R [Filter]
- Topic : Bayesian Statistics [Filter]
- Topic : Bioinformatics : Statistics [Filter]
- Topic : Genetics [Filter]
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Registered: 2011-10-11 08:51 |
4. LazyMLVA - This project automates assignment of MLVA (Multiple locus VNTR (Variable-Number-of-Tandem-Repeats) Analysis) types from files straight out of the sequencer.
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- Development Status : 2 - Pre-Alpha [Filter]
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Registered: 2010-01-08 10:31 |
5. 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.
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- 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 [Filter]
- Topic : Bayesian Statistics [Filter]
- Topic : Genetics [Filter]
- Topic : Graphical Models [Filter]
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Registered: 2011-01-07 17:53 |
6. Sublogo dendrograms - Sublogo dendrograms are statistical graphics that reveal correlation in biological sequence alignments.
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- Development Status : 5 - Production/Stable [Filter]
- Environment : Console (Text Based) [Filter]
- Environment : Web Environment [Filter]
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- License : OSI Approved : GNU General Public License (GPL) (Now Filtering)
- Natural Language : English [Filter]
- Operating System : POSIX : Linux [Filter]
- Programming Language : PHP [Filter]
- Programming Language : R [Filter]
- Programming Language : Unix Shell [Filter]
- Topic : Bioinformatics : Visualization [Filter]
- Topic : Genetics [Filter]
- Topic : Graphics : Plotting [Filter]
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Registered: 2009-06-19 09:14 |
7. 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.
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- Development Status : 5 - Production/Stable [Filter]
- Environment : Console (Text Based) [Filter]
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- Programming Language : R [Filter]
- Topic : Bioinformatics : Medical Science [Filter]
- Topic : Genetics [Filter]
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Registered: 2011-03-23 10:20 |
8. 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.
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- Development Status : 5 - Production/Stable [Filter]
- Environment : Console (Text Based) [Filter]
- Environment : X11 Applications [Filter]
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- License : OSI Approved : GNU General Public License (GPL) (Now Filtering)
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- Programming Language : R [Filter]
- Topic : Bioinformatics : Visualization [Filter]
- Topic : Genetics [Filter]
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Registered: 2010-01-08 16:59 |
9. LNA for stochastic kinetic models - An R package for likelihood-based inference of stochastic kinetic models using a Linear Noise Approximation.
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- Development Status : 3 - Alpha [Filter]
- License : OSI Approved : GNU General Public License (GPL) (Now Filtering)
- Operating System : POSIX [Filter]
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- Topic : Genetics [Filter]
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Registered: 2011-05-25 19:48 |
10. sonicLength - sonicLength estimates the abundances of cells marked with integrated DNA using DNA fragment length data. Also included are tools for random number generation apropos to fragment lengths, simulating datasets, and jackknifing multiple replicates
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- Development Status : 5 - Production/Stable [Filter]
- Environment : Console (Text Based) [Filter]
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- License : OSI Approved : GNU General Public License (GPL) (Now Filtering)
- Natural Language : English [Filter]
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- Programming Language : R [Filter]
- Topic : Bioinformatics : Medical Science [Filter]
- Topic : Bioinformatics : Statistics [Filter]
- Topic : Genetics [Filter]
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Registered: 2011-09-14 03:27 |
11. synbreed - Collection of statistical and genetic methods developed for the synbreed project for synergistic plant and animal breeding.
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- Development Status : 4 - Beta [Filter]
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- License : OSI Approved : GNU General Public License (GPL) (Now Filtering)
- Natural Language : English [Filter]
- Natural Language : German [Filter]
- Operating System : Microsoft : Windows [Filter]
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- Programming Language : R [Filter]
- Topic : Bioinformatics : Statistics [Filter]
- Topic : Bioinformatics : Visualization [Filter]
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Registered: 2010-03-05 10:51 |
12. 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'.
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- Development Status : 5 - Production/Stable [Filter]
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- Natural Language : English [Filter]
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- Programming Language : Fortran [Filter]
- Programming Language : R [Filter]
- Topic : Biostatistics & Medical Statistics [Filter]
- Topic : Genetics [Filter]
- Topic : Multivariate Statistics : Linear Models [Filter]
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Registered: 2011-11-10 03:57 |
13. plantbreeding - plantbreeding: R Software package for analysis and visualization of data from plant breeding and genetics experiments.
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- Natural Language : English [Filter]
- Operating System : Microsoft : Windows [Filter]
- Programming Language : R [Filter]
- Topic : Bioinformatics : Statistics [Filter]
- Topic : Design of Experiments & Analysis of Experimental Data [Filter]
- Topic : Genetics [Filter]
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Registered: 2012-07-01 21:32 |
14. 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.
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Registered: 2013-04-11 08:27 |
15. 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).
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- Development Status : 4 - Beta [Filter]
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- License : OSI Approved : GNU General Public License (GPL) (Now Filtering)
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- Programming Language : R [Filter]
- Topic : Genetics [Filter]
- Topic : Graphical Models [Filter]
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Registered: 2013-07-07 18:26 |
16. 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.
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- Development Status : 5 - Production/Stable [Filter]
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- Programming Language : Java [Filter]
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Registered: 2011-08-19 15:59 |
17. 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.
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- Topic : Bioinformatics : Statistics [Filter]
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Registered: 2013-12-19 15:12 |
18. cgen - Parallel Genomic Prediction and GWAS in R using Eigen and Rcpp
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- Topic : High Performance Computing [Filter]
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Registered: 2013-05-29 18:34 |
19. Priority Index - Priority Index or PI accelerates target selection through networking genetic evidence.
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Registered: 2016-04-21 23:06 |
