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http://gmc.mdc-berlin.de/alohomora/

Software application designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip(R) Human Mapping 10K Array. (entry from Genetic Analysis Software)

Proper citation: ALOHOMORA (RRID:SCR_009117) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/caspar.html

Software application who''s main novel feature is conditional linkage analyses, in which the population can be subdivided according to criteria at some loci and analyzed for linkage at other loci. CASPAR uses simulation to overcome the problems inherent in such multiple testing. (entry from Genetic Analysis Software)

Proper citation: CASPAR (RRID:SCR_009074) Copy   

•   Source: SciCrunch Registry

http://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-imprinting/index.html#c63682

Resource no longer in service. Documented on February 23,2021.Software tool as modification of GENEHUNTER software package . Allows for parametric multi-marker linkage analysis of dichotomous traits caused by imprinted genes. By specification of two heterozygote penetrance parameters, paternal and maternal origin of the disease allele can be treated differently in terms of probability of expression of the trait.

Proper citation: genehunter-imprinting (RRID:SCR_009104) Copy   

•   Source: SciCrunch Registry

http://associationviewer.vital-it.ch/

A Java application used to display SNPs in a genetic context. Supplementary data (such as genes or LD plots) is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks. (entry from Genetic Analysis Software)

Proper citation: ASSOCIATIONVIEWER (RRID:SCR_009063) Copy   

•   Source: SciCrunch Registry

http://www.rqtl.org

Software program for mapping quantitative trait loci in experimental crosses. (entry from Genetic Analysis Software)

Proper citation: R/QTL (RRID:SCR_009085) Copy   

•   Source: SciCrunch Registry

http://www.stat.washington.edu/thompson/Genepi/Albert/albert.shtml

Software application that estimates genotype relative risks, genotyping error rates and population risk allele frequencies from marker genotype data in case-parent trios. ALBERT uses the distribution of trio marker genotypes to compute maximum likelihood estimates for the parameters. (entry from Genetic Analysis Software)

Proper citation: ALBERT (RRID:SCR_009037) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/fastlink.html

Software application (entry from Genetic Analysis Software)

Proper citation: FASTLINK (RRID:SCR_009177) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/ExomePicks

Software application that suggests individuals to be sequenced in a large pedigree. ExomePicks assumes that a genotyping chip or another cost effective means will be used to determine IBD sharing in the pedigree and that, subsequently, one would like to sequence a minimal number of individuals and use their sequences together with IBD information to deduce the sequence of other individuals in the pedigree. We are currently using it in the context of whole exome and whole genome sequencing studies to pick individuals to be sequenced from large family collections. (entry from Genetic Analysis Software)

Proper citation: EXOMEPICKS (RRID:SCR_009174) Copy   

•   Source: SciCrunch Registry

http://kumasakanatsuhiko.jp/projects/disentangler/

Software application that is a visualization technique for linkage disequilibrium mapping and haplotype analysis of multiple multi-allelic genetic markers. (entry from Genetic Analysis Software)

Proper citation: DISENTANGLER (RRID:SCR_009161) Copy   

•   Source: SciCrunch Registry

https://github.com/OpenMendel/MendelIHT.jl

Software Julia package that implements iterative hard thresholding as multiple regression model for GWAS. Built-in support for handling PLINK and VCF files, parallel computing, fits a variety of GLM models, and handles grouping/weighting SNPs.

Proper citation: MendelIHT.jl (RRID:SCR_018292) Copy   

•   Source: SciCrunch Registry

https://bioconda.github.io/

Software distribution management for life sciences. Channel for Conda package manager specializing in bioinformatics software. Consists of repository of recipes hosted on GitHub, build system turning these recipes into conda packages, repository of packages containing bioinformatics packages ready to use with conda install.

Proper citation: BioConda (RRID:SCR_018316) Copy   

•   Source: SciCrunch Registry

https://github.com/mridulaprasad/CorrDrugTumorMSI

Software R pipeline to correlate drug distribution with tumor tissue types in mass spectrometry imaging data.

Proper citation: CorrDrugTumorMSI (RRID:SCR_018962) Copy   

•   Source: SciCrunch Registry

https://github.com/cobilab/geco3/

Software tool as DNA compressor that uses neural network to do mixing of experts.

Proper citation: GeCo3 (RRID:SCR_018877) Copy   

•   Source: SciCrunch Registry

https://github.com/liqiwei2000/BayesEpiModels

Software tool for accessing performance of different epidemiological models, including both growth and compartmental models, in Bayesian framework.

Proper citation: BayesEpiModels (RRID:SCR_019291) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-Chado-Schema

Standard object-relational mapping layer for use with GMOD Chado database schema. This layer is implemented with DBIx::Class, generated with the help of DBIx::Class::Schema::Loader module.

Proper citation: Bio-Chado-Schema (RRID:SCR_024059) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/AI-FANN

Software Perl wrapper for the Fast Artificial Neural Network library

Proper citation: AI-FANN (RRID:SCR_024060) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-Coordinate

Software application used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples.

Proper citation: Bio-Coordinate (RRID:SCR_024063) Copy   

•   Source: SciCrunch Registry

https://ginkgo-cadx.com/en/

Software advanced DICOM viewer and dicomizer that can also be used to convert png, jpeg, bmp, pdf, tiff to DICOM files.

Proper citation: Ginkgo CADx (RRID:SCR_024031) Copy   

•   Source: SciCrunch Registry

http://samtools.github.io/htsjdk/

Software implementation of unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing data. There are also an number of useful utilities for manipulating HTS data.

Proper citation: HTSJDK (RRID:SCR_024036) Copy   

•   Source: SciCrunch Registry

http://proteomics.ucsd.edu/Software/Inspect/

Software tool to addresses several algorithmic problems in order to identify modified proteins.Software MS/MS database search tool specifically designed to address two crucial needs of the proteomics comminuty: post-translational modification identification and search speed.

Proper citation: InsPecT (RRID:SCR_024038) Copy   

•   Source: SciCrunch Registry