Software Map

Project Tree

Project Tree

Now limiting view to projects in the following categories:
Intended Audience :: End Users/Desktop [Remove This Filter]

Topic > Genetics

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

Browse By:

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

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

Development Status : 4 - Beta [Filter]
Environment : Console (Text Based) [Filter]
Intended Audience : Developers [Filter]
Intended Audience : End Users/Desktop (Now Filtering)
License : OSI Approved : GNU General Public License (GPL) [Filter]
Natural Language : English [Filter]
Natural Language : German [Filter]
Operating System : MacOS [Filter]
Operating System : Microsoft : Windows [Filter]
Operating System : POSIX : Linux [Filter]
Programming Language : C/C\+\+ [Filter]
Programming Language : R [Filter]
Topic : Bioinformatics [Filter]
Topic : Genetics [Filter]
Topic : High Performance Computing [Filter]

Activity Percentile: 0.00

Registered: 2013-05-29 18:34

1. 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]
Intended Audience : End Users/Desktop (Now Filtering)
License : OSI Approved : GNU General Public License (GPL) [Filter]
Natural Language : English [Filter]
Operating System : MacOS [Filter]
Operating System : Microsoft : Windows [Filter]
Operating System : POSIX : Linux [Filter]
Programming Language : C/C\+\+ [Filter]
Programming Language : R [Filter]
Topic : Bioinformatics : Medical Science [Filter]
Topic : Genetics [Filter]

Activity Percentile: 0.00

Registered: 2011-03-23 10:20

2. 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]
Intended Audience : End Users/Desktop (Now Filtering)
License : OSI Approved : GNU General Public License (GPL) [Filter]
Natural Language : English [Filter]
Natural Language : French [Filter]
Programming Language : C/C\+\+ [Filter]
Programming Language : R [Filter]
Topic : Bioinformatics [Filter]
Topic : Database : R Interfaces [Filter]
Topic : Genetics [Filter]

Activity Percentile: 0.00

Registered: 2008-07-28 09:03

3. 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]
Intended Audience : End Users/Desktop (Now Filtering)
License : OSI Approved : GNU General Public License (GPL) [Filter]
Natural Language : English [Filter]
Operating System : MacOS [Filter]
Operating System : Microsoft : Windows [Filter]
Operating System : POSIX : Linux [Filter]
Programming Language : R [Filter]
Topic : Bioinformatics : Visualization [Filter]
Topic : Genetics [Filter]

Activity Percentile: 0.00

Registered: 2010-01-08 16:59

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.
Development Status : 2 - Pre-Alpha [Filter] Environment : Console (Text Based) [Filter] Intended Audience : End Users/Desktop (Now Filtering) License : OSI Approved : GNU General Public License (GPL) [Filter] Natural Language : English [Filter] Operating System : OS Independent [Filter] Programming Language : R [Filter] Topic : Bioinformatics [Filter] Topic : Genetics [Filter]	Activity Percentile: 0.00 Registered: 2010-01-08 10:31

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

Development Status : 5 - Production/Stable [Filter]
Environment : Console (Text Based) [Filter]
Environment : Web Environment [Filter]
Environment : Win32 (MS Windows) [Filter]
Intended Audience : Developers [Filter]
Intended Audience : End Users/Desktop (Now Filtering)
License : OSI Approved : BSD License [Filter]
License : Other/Proprietary License [Filter]
Natural Language : English [Filter]
Operating System : Microsoft : Windows : Windows NT/2000/XP [Filter]
Operating System : Other OS [Filter]
Operating System : POSIX : Linux [Filter]
Programming Language : R [Filter]
Topic : Bioinformatics : Visualization [Filter]
Topic : Genetics [Filter]
Topic : High Performance Computing [Filter]

Activity Percentile: 0.00

Registered: 2019-07-16 15:34

6. 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]
Intended Audience : Developers [Filter]
Intended Audience : End Users/Desktop (Now Filtering)
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 : R [Filter]
Topic : Bayesian Statistics [Filter]
Topic : Bioinformatics : Statistics [Filter]
Topic : Genetics [Filter]

Activity Percentile: 0.00

Registered: 2011-10-11 08:51

7. 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

Development Status : 5 - Production/Stable [Filter]
Environment : Console (Text Based) [Filter]
Intended Audience : End Users/Desktop (Now Filtering)
License : OSI Approved : GNU General Public License (GPL) [Filter]
Natural Language : English [Filter]
Operating System : OS Independent [Filter]
Programming Language : R [Filter]
Topic : Bioinformatics : Medical Science [Filter]
Topic : Bioinformatics : Statistics [Filter]
Topic : Genetics [Filter]

Activity Percentile: 0.00

Registered: 2011-09-14 03:27

8. 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 (Now Filtering) License : OSI Approved : GNU General Public License (GPL) [Filter] Natural Language : English [Filter] Operating System : POSIX : Linux [Filter] Programming Language : R [Filter] Topic : Bioinformatics [Filter] Topic : Genetics [Filter]	Activity Percentile: 0.00 Registered: 2011-08-17 20:46

9. 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]
Intended Audience : End Users/Desktop (Now Filtering)
Intended Audience : Other Audience [Filter]
License : OSI Approved : BSD License [Filter]
Natural Language : English [Filter]
Operating System : OS Independent [Filter]
Programming Language : R [Filter]
Topic : Bioinformatics [Filter]
Topic : Genetics [Filter]
Topic : Multivariate Statistics [Filter]

Activity Percentile: 0.00

Registered: 2011-02-02 00:51

10. 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]
Intended Audience : End Users/Desktop (Now Filtering)
License : OSI Approved : GNU General Public License (GPL) [Filter]
Natural Language : English [Filter]
Natural Language : German [Filter]
Operating System : Microsoft : Windows [Filter]
Operating System : POSIX : Linux [Filter]
Programming Language : R [Filter]
Topic : Bioinformatics : Statistics [Filter]
Topic : Bioinformatics : Visualization [Filter]
Topic : Genetics [Filter]

Activity Percentile: 0.00

Registered: 2010-03-05 10:51

11. 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 (Now Filtering)
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 [Filter]
Topic : Biostatistics & Medical Statistics [Filter]
Topic : Genetics [Filter]
Topic : Multivariate Statistics : Linear Models [Filter]

Activity Percentile: 0.00

Registered: 2011-11-10 03:57

12. 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 (Now Filtering) Programming Language : R [Filter] Topic : Bioinformatics [Filter] Topic : Biostatistics & Medical Statistics [Filter] Topic : Genetics [Filter]	Activity Percentile: 0.00 Registered: 2012-04-18 14:21

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

Development Status : 3 - Alpha [Filter]
Intended Audience : Developers [Filter]
Intended Audience : End Users/Desktop (Now Filtering)
License : OSI Approved : GNU General Public License (GPL) [Filter]
Natural Language : English [Filter]
Operating System : MacOS [Filter]
Operating System : Microsoft : Windows [Filter]
Operating System : POSIX : Linux [Filter]
Programming Language : R [Filter]
Topic : Bioinformatics [Filter]
Topic : Genetics [Filter]
Topic : Software Development [Filter]

Activity Percentile: 0.00

Registered: 2016-04-21 23:06

14. Parent-specific DNA copy numbers (abo) - Paired PSCBS: Parent-specific copy number in paired tumor-normal studies using circular binary segmentation (CBS). Packages in this project: PSCBS.
Development Status : 3 - Alpha [Filter] Development Status : 4 - Beta [Filter] Intended Audience : Developers [Filter] Intended Audience : End Users/Desktop (Now Filtering) Natural Language : English [Filter] Operating System : OS Independent [Filter] Programming Language : R [Filter] Topic : Bioinformatics [Filter] Topic : Genetics [Filter]	Activity Percentile: 0.00 Registered: 2009-10-20 01:21

15. 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]
Environment : Console (Text Based) [Filter]
Environment : No Input/Output (Daemon) [Filter]
Environment : Web Environment [Filter]
Intended Audience : Developers [Filter]
Intended Audience : End Users/Desktop (Now Filtering)
License : OSI Approved : GNU Lesser General Public License (LGPL) [Filter]
License : Other/Proprietary License [Filter]
Natural Language : English [Filter]
Operating System : OS Independent [Filter]
Programming Language : R [Filter]
Topic : Bioinformatics [Filter]
Topic : Database [Filter]
Topic : Genetics [Filter]

Activity Percentile: 0.00

Registered: 2009-05-19 20:01

16. 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]
Intended Audience : End Users/Desktop (Now Filtering)
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 [Filter]
Programming Language : Unix Shell [Filter]
Topic : Bioinformatics : Visualization [Filter]
Topic : Genetics [Filter]
Topic : Graphics : Plotting [Filter]

Registered: 2009-06-19 09:14

17. 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]
Intended Audience : Developers [Filter]
Intended Audience : End Users/Desktop (Now Filtering)
License : OSI Approved : GNU General Public License (GPL) [Filter]
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]

Activity Percentile: 0.00

Registered: 2011-01-07 17:53

18. 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]
Intended Audience : End Users/Desktop (Now Filtering)
License : OSI Approved : GNU General Public License (GPL) [Filter]
License : OSI Approved : GNU Lesser General Public License (LGPL) [Filter]
Natural Language : English [Filter]
Operating System : OS Independent [Filter]
Programming Language : C/C\+\+ [Filter]
Programming Language : R [Filter]
Topic : Bioinformatics [Filter]
Topic : Genetics [Filter]
Topic : Software Development [Filter]

Activity Percentile: 0.00

Registered: 2013-04-11 08:27

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 (Now Filtering) License : OSI Approved : GNU General Public License (GPL) [Filter] Natural Language : English [Filter] Operating System : OS Independent [Filter] Programming Language : R [Filter] Topic : Genetics [Filter] Topic : Graphical Models [Filter]	Activity Percentile: 0.00 Registered: 2013-07-07 18:26

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