Tools   Select Another Resource Report Type

http://cougar.fhcrc.org/hplus/

An analysis tool for performing haplotype estimation on genetic markers such as SNPs and microsatellites. It is able to handle datasets that include case-control status as well as covariates and marker location variables (such as gene name, chromosome location, etc). (entry from Genetic Analysis Software)

Proper citation: HPLUS (RRID:SCR_009239) Copy   

•   Source: SciCrunch Registry

http://galton.uchicago.edu/genehunterplus

Software application that is a modification of the GENEHUNTER software package which produces output files containing the null and conditional distributions of the test statistic (in nullprobs.dat and probs.dat, respectively). These files can then be used as input to the ASM program which incorporates the allele sharing modeling for lodscores and likelihood ratio tests as developed by Kong and Cox (1997). (entry from Genetic Analysis Software)

Proper citation: GENEHUNTER-PLUS (RRID:SCR_009193) Copy   

•   Source: SciCrunch Registry

http://www.biostat.jhsph.edu/~wmchen/gf.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 21, 2016. Software application that uses GEE method to estimate the location of the susceptibility gene based on the allele-sharing of affected sib pairs for multiple markers. GENEFINDER can further the analysis of GENEHUNTER by providing a more accurate gene location estimation and the corresponding confidence interval.

Proper citation: GENEFINDER (RRID:SCR_009190) Copy   

•   Source: SciCrunch Registry

http://hg-wen.uchicago.edu/selection/haplotter.htm

A web application that has been developed to display the results of a scan for positive selection in the human genome using the HapMap data. It can be used as a resource to examine various population genetic measures in a genomic region. Measures that are currently displayed include iHS (a statistic developed to detect recent positive selection), Fay and Wu''s H, Tajima''s D and Fst. (entry from Genetic Analysis Software)

Proper citation: HAPLOTTER (RRID:SCR_009229) Copy   

•   Source: SciCrunch Registry

http://mayoresearch.mayo.edu/mayo/research/biostat/schaid.cfm

A suite of routines for the analysis of indirectly measured haplotypes. (entry from Genetic Analysis Software)

Proper citation: HAPLO.STAT (RRID:SCR_009227) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.med.yale.edu/group/software.html

Software application for haplotype reconstruction in general pedigree without recombination (entry from Genetic Analysis Software)

Proper citation: HAPLORE (RRID:SCR_009226) Copy   

•   Source: SciCrunch Registry

http://www.angelfire.com/mn2/nath/gems.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for fitting Genetic Epidemiology Models by running stochastic simulation in relation to disease dynamics.

Proper citation: GEMS (RRID:SCR_009188) Copy   

•   Source: SciCrunch Registry

http://medicine.iupui.edu/neph/obrien/digital

Core facility which develops and implements software and methods of image segmentation for fluorescence microscopy data.

Proper citation: Indiana O'Brien Center for Advanced Microscopic Analysis Digital Image Analysis Core (RRID:SCR_015276) Copy   

•   Source: SciCrunch Registry

http://cihd.cores.utah.edu/mgd/

Core facility which provides custom TALEN and Crispr-Cas9 DNA nucleases to induce targeted mutations in a genomic region of interest. It also provides hardware, reagents, and expertise for optimizing and performing HRMA for genes of interest.

Proper citation: Center for Iron and Heme Disorders at the University of Utah Mutation Generation and Detection Core (RRID:SCR_015339) Copy   

•   Source: SciCrunch Registry

http://www.cancer.iu.edu/research-trials/facilities/flow-cytometry/index.shtml

Core facility which provides flow cytometry consultation, technical advice, flow cytometric analysis and cell sorting services as well as flow cytometric image analysis.

Proper citation: Indiana University School of Medicine Flow Cytometry Core Facility (RRID:SCR_015346) Copy   

•   Source: SciCrunch Registry

https://medicine.uiowa.edu/genetherapy/vector-core

Core facility which provides support to cystic fibrosis investigators in gene transfer technologies through consultation, development of novel vectors, collaborative testing of vectors for function and purity, and routine vector preparations.

Proper citation: University of Iowa Center for Gene Therapy Vectore Core (RRID:SCR_015417) Copy   

•   Source: SciCrunch Registry

http://www.mmpc.org/shared/showCenterCore.aspx?id=30

Core that provides investigators with services to accurately measure the major components of energy balance in their mouse models and tests that allow investigators to examine physiological factors that may influence food intake or energy expenditure.

Proper citation: MMPC-University of California Davis Energy Balance Exercise and Behavior Core (RRID:SCR_015364) Copy   

•   Source: SciCrunch Registry

http://www.mmpc.org/shared/showCenterCore.aspx?id=37

Core that offers measurement of gut permeability, plasma lipopolysaccharide binding protein (LBP) assay, and inflammatory profiling.

Proper citation: MMPC-University of California Davis Microbiome and Host Response Core (RRID:SCR_015361) Copy   

•   Source: SciCrunch Registry

http://depts.washington.edu/cfrtc/genomics/

Core provides genomics-based tools, data management and analysis tools, and creates platforms that integrate data from the Clinical and Immunology Cores for human samples and bacterial isolates. Services include consultation and experimental design assistance for using new-generation sequencing technology, data analysis, bioinformatic support, data access and storage, high throughput and new-generation whole-genome sequencing, and RNA-seq analysis of transcriptomes.

Proper citation: University of Washington Genomics Core Cystic Fibrosis Research Translation Center and Research Development Program (RRID:SCR_015404) Copy   

•   Source: SciCrunch Registry

http://www.med.upenn.edu/molecular/core_morphology.shtml

Core facility that provides histological services, equipment usage, and technical expertise to digestive and liver research projects.

Proper citation: University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Molecular Pathology and Imaging Core (RRID:SCR_015618) Copy   

•   Source: SciCrunch Registry

http://sph.unc.edu/norc/animal/

Core that offers technical support and expertise for measuring traits related to metabolism in mouse models of obesity and nutritionally relevant disease. It provides access to methods, equipment, and populations to support high quality and high throughput phenotyping of energy balance components in mice.

Proper citation: University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Animal Metabolism Phenotyping Core (RRID:SCR_015465) Copy   

•   Source: SciCrunch Registry

http://www.microbesonline.org/fasttree/

Source code that infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT, WAG, or LG models of amino acid evolution.

Proper citation: FastTree (RRID:SCR_015501) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/phytools/index.html

Software R package for phylogenetic comparative biology. The package contains various functions for phylogenetic analysis of comparative data from species.

Proper citation: phytools (RRID:SCR_015502) Copy   

•   Source: SciCrunch Registry

https://github.com/lucventurini/mikado/

Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to select the best models in each locus.

Proper citation: Mikado (RRID:SCR_016159) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/msm/index.html

Source code for fitting continuous-time Markov and hidden Markov multi-state models to longitudinal data. It was originally designed for processes observed at arbitrary times in continuous time but some other observation schemes are supported. Both Markov transition rates and the hidden Markov output process can be modelled in terms of covariates, which may be constant or piecewise-constant in time.

Proper citation: MSM (RRID:SCR_015500) Copy   

•   Source: SciCrunch Registry