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on page 1 showing 20 out of 1,486 results

Cite this (1000 Fungal Genome Project, RRID:SCR_016463)

URL: https://genome.jgi.doe.gov/programs/fungi/1000fungalgenomes.jsf

Resource Type: Resource, topical portal, data access protocol, database, web service, organism-related portal, portal, software resource, project portal, data or information resource

Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment.

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Cite this (16p_resource Code, RRID:SCR_016845)

URL: http://www.github.com/kmuench/16p_resource

Resource Type: Resource, software resource, source code

Software tool as a code to support figure generation for the manuscript by Roth, Muench et al. Used to perform analysis.

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    2DMAP

Cite this (2DMAP, RRID:SCR_009036)

URL: http://www.genlink.wustl.edu/software

Resource Type: Resource, software resource, software application

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for constructing 2-d crossover-based map.

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    2LD

Cite this (2LD, RRID:SCR_000826)

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

Resource Type: Resource, software resource, software application

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software program for calculating linkage disequilibrium (LD) measures between two polymorphic markers.

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    2SNP

Cite this (2SNP, RRID:SCR_009038)

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

Resource Type: Resource, software resource, software application

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

  • From Current Category

Cite this (Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal, RRID:SCR_003743)

URL: http://www.type2diabetesgenetics.org/

Resource Type: Resource, disease-related portal, topical portal, database, service resource, portal, storage service resource, data repository, data or information resource

Portal and database of DNA sequence, functional and epigenomic information, and clinical data from studies on type 2 diabetes and analytic tools to analyze these data. .Provides data and tools to promote understanding and treatment of type 2 diabetes and its complications. Used for identifying genetic biomarkers correlated to Type 2 diabetes and development of novel drugs for this disease.

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    AceView

Cite this (AceView, RRID:SCR_002277)

URL: http://www.ncbi.nlm.nih.gov/ieb/research/acembly/

Resource Type: Resource, data or information resource, database

THIS RESOURCE IS NO LONGER SUPPORTED, documented August 29, 2016. AceView offers an integrated view of the human, nematode and Arabidopsis genes reconstructed by co-alignment of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes and their functions and to stimulate further validating experiments at the bench. AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals' transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated. Our goals are to offer an up-to-date resource on the genes, in the hope to stimulate further experiments at the bench, or to help medical research. AceView can be queried by meaningful words or groups of words as well as by most standard identifiers, such as gene names, Entrez Gene ID, UniGene ID, GenBank accessions.

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Cite this (ACGT Inc., RRID:SCR_001026)

URL: http://www.acgtinc.com

Resource Type: Resource, analysis service resource, service resource, production service resource

Company which provides a suite of molecular biology and genomic services, including DNA sequencing by Sanger and Next Generation Sequencing. All services are offered at a research, GLP or clinical grade levels.

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Cite this (Acquisition and Analysis for Electron Tomography, RRID:SCR_000192)

URL: http://www.biochem.mpg.de/en/rd/baumeister/research/ContentCEM/Software_development

Resource Type: Resource, software resource, software toolkit

A software platform for low dose electron tomography (ET) for all processing steps: acquisition, alignment, reconstruction, and analysis. Requires: Matlab R2008a and Image Processing Toolbox (V6.1)

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    ACT

Cite this (ACT, RRID:SCR_009033)

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

Resource Type: Resource, software resource, software application

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)

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    ADAPT

Cite this (ADAPT, RRID:SCR_006769)

URL: http://bmsr.usc.edu/software/adapt/

Resource Type: Resource, software resource, software application, simulation software, data processing software, data analysis software

Computational modeling platform developed for pharmacokinetic and pharmacodynamic applications. It is intended for basic and clinical research scientists and is designed to facilitate the discovery, exploration and application of the underlying pharmacokinetic and pharmacodynamic properties of drugs. Features in ADAPT 5
*Individual Analysis ** Estimation module (ID) includes weighted least squares, maximum likelihood (ML), generalized least squares (GLS), maximum a posterior Bayesian estimation (MAP) ** Simulation module (SIM) includes capabilities for single and multisubject simulations ** Sample schedule design module (SAMPLE) provides the ability to calculate D- and C-optimal designs * Population Analysis ** Parametric population PK/PD modeling using maximum likelihood estimation via the EM algorithm with sampling (MLEM), as introduced by Schumitzky (1995) and by Walker (1996), with extensions and enhancements by Bauer & Guzy (2004). ** Iterated two-stage (ITS) analysis as proposed by Prevost (1977) and Steimer, Mallet and colleagues (1984). ** Convenient standard two-stage (STS) and naive pooled data (NPD) modeling, each with WLS, ML, and MAP estimators. System Requirements * Operating System: Windows XP/Vista/7 * Other Software REQUIRED: Intel Visual Fortran 10.x XE2013

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    ADEGENET

Cite this (ADEGENET, RRID:SCR_000825)

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

Resource Type: Resource, software resource, software application

Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software)

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Cite this (ADInstruments - Data Acquisition Systems for Life Science, RRID:SCR_001620)

URL: http://www.adinstruments.com/products/software/modules/neuro_explorer.php

Resource Type: Organization, material resource, instrument supplier

THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 19, 2018; A provider of computer-based data acquisition and analysis systems for life science. Products enable users to record and analyze life science data quickly and efficiently. ADInstruments product range is based on the PowerLab data acquisition system with LabChart software. The PowerLab system (also MacLab) is used in universities, hospitals, research institutes, pharmaceutical companies, contract research organizations and other private industry research sectors.

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    ADMIXMAP

Cite this (ADMIXMAP, RRID:SCR_009035)

URL: http://www.homepages.ed.ac.uk/pmckeigu/admixmap/index.html

Resource Type: Resource, software resource, software application

General-purpose program for modelling admixture, using marker genotypes and trait data on a sample of individuals from an admixed population (such as African-Americans), where the markers have been chosen to have extreme differentials in allele frequencies between two or more of the ancestral populations between which admixture has occurred. The main difference between ADMIXMAP and classical programs for estimation of admixture such as ADMIX is that ADMIXMAP is based on a multilevel model for the distribution of individual admixture in the population and the stochastic variation of ancestry on hybrid chromosomes. This makes it possible to model the associations of ancestry between linked marker loci, and the association of a trait with individual admixture or with ancestry at a linked marker locus. (entry from Genetic Analysis Software)

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Cite this (Advanced Neuroscience Imaging Research Laboratory Software Packages, RRID:SCR_002926)

URL: http://www.fmri.wfubmc.edu/cms/software

Resource Type: Resource, software resource, software toolkit

Research group based in the Department of Radiology of Wake Forest University School of Medicine devoted to the application of novel image analysis methods to research studies. The ANSIR lab also maintains a fully-automated functional and structural image processing pipeline supporting the image storage and analysis needs of a variety of scientists and imaging studies at Wake Forest. Software packages and toolkits are currently available for download from the ANSIR Laboratory, including: WFU Biological Parametric Mapping Toolbox, WFU_PickAtlas, and Adaptive Staircase Procedure for E-Prime.

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    affydata

Cite this (affydata, RRID:SCR_016976)

URL: http://bioconductor.org/packages/release/data/experiment/html/affydata.html

Resource Type: Resource, software resource, software application, data analysis software, data processing software, data or information resource

Software R package for analysis of Affymetrix Data. Contains samples data files of a large size.

  • From Current Category

    affy

Cite this (affy, RRID:SCR_012835)

URL: http://www.bioconductor.org/packages/release/bioc/html/affy.html

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis.

  • From Current Category

    AGEINF

Cite this (AGEINF, RRID:SCR_009039)

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

Resource Type: Resource, software resource, software application

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

  • From Current Category

Cite this (Agilent G2565CA Microarray Scanner, RRID:SCR_017206)

URL: https://www.chem-agilent.com/contents.php?id=1000947

Resource Type: Resource, material resource

Part of microarray analysis solution from Agilent Technologies. Laser induced fluorescence scanner designed to read microarrays printed on standard slides. Measures fluorescence intensity of labeled sample nucleic acid bound to microarrays.

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Cite this (Agilent Masshunter Qualitative Analysis, RRID:SCR_016657)

URL: https://www.agilent.com/en/products/software-informatics/masshunter-suite/masshunter-qualitative-analysis-gcms

Resource Type: Resource, data analysis software, data processing software, software application, data analytics software, software toolkit, software resource, data acquisition software

Software tools for compound-centric data mining and navigation. Used to identify compounds in overlapping and co-eluting peaks with feature extraction and correlation algorithms for chromatographic separation. Used for separating true signals from noise.

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