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http://www.uni-bonn.de/~umt70e/soft.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application for calculation of the restricted likelihood-ratio affected sib-pair test for linkage allowing for imprinting (entry from Genetic Analysis Software)

Proper citation: ILR (RRID:SCR_007895) Copy   

•   Source: SciCrunch Registry

https://github.com/gaow/genetic-analysis-software/blob/master/pages/2SNP.md

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. An algorithm resource for scalable phasing method for trios and unrelated individuals.

Proper citation: 2SNP (RRID:SCR_009038) Copy   

•   Source: SciCrunch Registry

https://github.com/gaow/genetic-analysis-software/blob/master/pages/AGEINF.md

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application used to infer the age of a rare, selectively-neutral mutation.

Proper citation: AGEINF (RRID:SCR_009039) 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.mapmanager.org/mmQT.html

A graphic, interactive program to map quantitative trait loci by regression methods; MAP MANAGER CLASSIC enhanced by quantitative trait mapping. (entry from Genetic Analysis Software)

Proper citation: MAP MANAGER QT (RRID:SCR_008101) Copy   

•   Source: SciCrunch Registry

http://www.epigenetic.org/Linkage/act.html,

Software application that contains the following modules: ibd, calculates the proportion of gene shared identical by decent for a nuclear family; ibdn, (modified program of ERPA), which implements a method for assessing increased-allele sharing between all pairs of affected relatives within a pedigree; multic, multivariate analysis for complex traits; ml, estimation of variance components using maximum likelihood; ql, estimation of variance components using quasi likelihood; relcov, generates first degree relationship coefficients for extended families; sim2s, the simulation program that was used to test ACT; cage, Cohort Analysis for Genetic Epidemiology; gh: GeneHunter, heavily modified to assist multipoint calculation using multic; TDT: TDT programs written in SAS; gcc and f77 compilers are necessary. Executable programs are included for compatible operating systems, i.e., Solaris2.6. (entry from Genetic Analysis Software)

Proper citation: ACT (RRID:SCR_009033) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 15, 2017. Software application (entry from Genetic Analysis Software)

Proper citation: S (RRID:SCR_007646) Copy   

•   Source: SciCrunch Registry

http://www.chgb.org.cn/lda/lda.htm

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A Java program for analyzing the pairwise linkage disequilibrium.

Proper citation: LDA (RRID:SCR_007527) Copy   

•   Source: SciCrunch Registry

http://www-gene.cimr.cam.ac.uk/clayton/software/

Software program for estimating frequencies of haplotypes of large numbers of diallelic markers from unphased genotype data from unrelated subjects (entry from Genetic Analysis Software)

Proper citation: SNPHAP (RRID:SCR_008456) Copy   

•   Source: SciCrunch Registry

http://cmpg.unibe.ch/software/simcoal/

Software application (entry from Genetic Analysis Software)

Proper citation: SIMCOAL (RRID:SCR_008450) Copy   

•   Source: SciCrunch Registry

http://www.cpgr.org.za

Services to life science and biotech communities in South Africa. Based in Cape Town, combine information about genomic and proteomic technologies with bio computational pipelines to create fit for purpose offerings for customers in academia and industry.

Proper citation: University of Cape Town Centre for Proteomic and Genomic Research (CPGR) Core Facility (RRID:SCR_017158) Copy   

•   Source: SciCrunch Registry

https://dnacore.missouri.edu/

Core research facility providing genomic services that include next generation sequencing , single cell sequencing, metagenomic, targeted amplicon sequencing, and Sanger sequencing.

Proper citation: University of Missouri-Columbia DNA Core Facility (RRID:SCR_017778) Copy   

•   Source: SciCrunch Registry

https://genome.duke.edu/cores-and-services/sequencing-and-genomic-technologies

Basic research oriented core provides genomic services.Services include Next Generation Sequencing Solutions,DNA and RNA sequencing, Illumina, PacBio, NGS Library preparation including single-cell RNA-seq, Nucleic Acid Extraction Services, total RNA extraction from blood samples in PAXgene tubes, total RNA extractions from cell pellets and miRNA extraction from serum/plasma.

Proper citation: Duke University Sequencing and Genomic Technologies Core Facility (RRID:SCR_017748) Copy   

•   Source: SciCrunch Registry

http://dmpi.duke.edu/molecular-genomics-shared-resource

Core offers variety of experimental platforms to facilitate genomics research. Accredited as Duke Shared Resource facility offers experience with genetic, genomic and epigenomic study design and technology, working closely with researchers to customize experiments to meet their needs. Applications include 10x Genomics NGS library generation for both single cell and gDNA experiments, DNA methylation microarrays, SNP genotyping and copy number microarrays, and Taqman targeted SNP genotyping.

Proper citation: Duke University Molecular Genomics Core Facility (RRID:SCR_017860) Copy   

•   Source: SciCrunch Registry

https://escore.ucsf.edu/

Core provides ES cell services with high probability of germline transmission. Offers ES cell targeting, genomic DNA extraction from 96-well plates, expansion of targeted ES cells, chromosome counts, and preparation of ES cells for microinjection.Prior to initiation of project, consultation is available on entire procedures of generating knockout mice. Core works with Gladstone Transgenic Gene Targeting Core for your microinjections to deliver full-range gene targeting service;CRISPR gRNA cloning,Cell-based functional test to identify best-performing TALENs or sgRNAs for your gene-editing experiment via mismatch-based assays such as Surveyor or T7E1;In vitro RNA synthesis - can help to make RNAs for your zygote injection or RNA transfection. We have TALEN and Cas9 plasmids with either T7 or T3 promoter subcloned in for efficient in vitro synthesis.sgRNAs for CRISPR can be synthesized off T7-sgRNA PCR product. Quality of synthesized RNAs will be checked via bioanalyzer;Custom TALEN to make double-strand breaks in genome;ES cell targeting (feeder-independent).Investigators targeting construct will be electroporated by core personnel. We have two feeder-independent ES cell lines, E14 (129-derived) and JM8A3.N1 (C57BL/6-derived) you can choose from. After drug selection for about one week, up to 300 colonies will be picked. When they are about to be confluent, we will split them as duplicate, one master plate to freeze for future expansion of positive clones and one plate for genotyping to identify targeted ES cell clones. Your plates for genotyping will be ready for pick-up 2-3 weeks after electroporation date.Genomic DNA extraction from ES cells on 96-well plate;Expansion of targeted clones from core targeting (up to 5 clones),A maximum of 5 positive clones will be thawed from 96-well plates and expanded to 6-wells. We will freeze 5 vials (each about 1 million)/clone for future use and give you 1 vial-equivalent cells to validate your genotyping before injection. It takes about 10 days to expand and freeze down cells;Expansion of ES cells from outside resources (per clone) Investigators provide one vial of frozen ES cells with information about culture condition from original resource. We will revive, nurture, and refreeze ES cells (5 vials) when they are ready. In addition, we will give you 1~2 million cells for your genotyping verification;Preparation for microinjection;Chromosome counting;Custom services.

Proper citation: University of California at San Francisco Embryonic Stem Cell Targeting Core Facility (RRID:SCR_017902) Copy   

•   Source: SciCrunch Registry

https://www.bi.vt.edu/services/genomics-sequencing-center

Core for development and application of Next-Generation Sequencing technologies. Provides experimental design consultation, and genomic, transcriptomic, and functional-genomics services. Specializes in development and application of Next-Generation Sequencing technologies and bioinformatics analyses. Instruments include Illumina NovaSeq 6000, Illumina NextSeq 500,Illumina MiSeq,Thermo Ion S5. Services include mRNA-Seq: Stranded and non-stranded, high levels of multiplexing up to 96 or more samples on NovaSeq;Standard amounts, Stranded-Seq: 500 ng total RNA, RIN 8;Low Input amounts, Stranded-Seq: 5 ng to 100 ng total RNA;Ultra Low Input amounts, Non-Stranded-Seq: 1-1000 cells or 10 pg - 10 ng;Total RNA-Seq - Stranded: 5-250 ng;Small RNA-Seq: 1 ug, multiplexing up to 48 samples/NextSeq run;Partially degraded samples - Stranded and Non-Stranded: LCM, FFPE samples, both stranded and non-stranded, 50 -100 ng;Microbial rRNA depletion and RNA-Seq with amounts as low as 1-5 ug of total RNA;Whole Genome Sequencing;Human / Animal / Plant;Microbial;As low as 1 ng De novo Sequencing;Exome/Targeted capture re-sequencing: Enables high sequencing depths;Agilent and Illumina platforms;Human, Mouse, Canine and other species;Targeted re-sequencing: High levels of multiplexing up to 200 samples / MiSeq run;PCR Amplicon sequencing;Illumina and Agilent platforms;ChIP-Seq;Transcription factor analysis;Histone modifications;DNA Methylation;MeDIP- and MBD-Seq;MethylC-Seq;Agilent SureSelect MethylC-Seq;Nucleosome Mapping;FAIRE-Seq and DNAse I-Seq;16S / 18S / ITS amplicon sequencing;Whole Genome Metagenomic sequencing;Metatranscriptomic analysis;DNA/chromatin fragmentation by Covaris DNA / RNA quality analysis: BioAnalyzer / TapeStation assay, Qubit (Picogreen) assays;qPCR services.

Proper citation: Virginia Tech Biocomplexity Institute Genomics Sequencing Center Core Facility (RRID:SCR_017958) Copy   

•   Source: SciCrunch Registry

http://cqls.oregonstate.edu/

Formerly Center for Genome Research and Biocomputing Core Facility. Functions and facilities include services in genomics, functional genomics, genotyping and imaging.Biocomputing facilities with computing infrastructure, which includes managed cloud and shared resources, data analyses and training are customized to individual needs, including genome assembly and annotation, analysis of RNAseq, GBS, and metagenomics data, and GPU-enabled deep learning analyses.

Proper citation: Oregon State University Center for Quantitative Life Sciences Core Facility (RRID:SCR_018373) Copy   

•   Source: SciCrunch Registry

http://www.salk.edu/science/core-facilities/integrative-genomics-and-bioinformatics-core/

Core facility established to assist the Salk community with integrating genomics data into their research. The primary focus of the core is to provide analysis support for next-generation sequencing applications.

Proper citation: Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility (IGC) (RRID:SCR_014842) Copy   

•   Source: SciCrunch Registry

http://atlasgeneticsoncology.org/

Online journal and database devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases. Its aim is to cover the entire field under study and it presents concise and updated reviews (cards) or longer texts (deep insights) concerning topics in cancer research and genomics.

Proper citation: Atlas of Genetics and Cytogenetics in Oncology and Haematology (RRID:SCR_007199) Copy   

•   Source: SciCrunch Registry

http://igs-server.cnrs-mrs.fr/mgdb/Rickettsia/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. Rickettsia are obligate intracellular bacteria living in arthropods. They occasionally cause diseases in humans. To understand their pathogenicity, physiologies and evolutionary mechanisms, RicBase is sequencing different species of Rickettsia. Up to now we have determined the genome sequences of R. conorii, R. felis, R. bellii, R. africae, and R. massiliae. The RicBase aims to organize the genomic data to assist followup studies of Rickettsia. This website contains information on R. conorii and R. prowazekii. A R. conorii and R. prowazekii comparative genome map is also available. Images of genome maps, dendrogram, and sequence alignment allow users to gain a visualization of the diagrams.

Proper citation: Rickettsia Genome Database (RRID:SCR_007102) Copy   

•   Source: SciCrunch Registry