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on page 1 showing 20 out of 1,916 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 (1000 Genomes: A Deep Catalog of Human Genetic Variation, RRID:SCR_006828)

URL: http://www.1000genomes.org/

Resource Type: Resource, organization portal, database, consortium, data set, portal, data or information resource

International collaboration producing an extensive public catalog of human genetic variation, including SNPs and structural variants, and their haplotype contexts, in an effort to provide a foundation for investigating the relationship between genotype and phenotype. The genomes of about 2500 unidentified people from about 25 populations around the world were sequenced using next-generation sequencing technologies. Redundant sequencing on various platforms and by different groups of scientists of the same samples can be compared. The results of the study are freely and publicly accessible to researchers worldwide. The consortium identified the following populations whose DNA will be sequenced: Yoruba in Ibadan, Nigeria; Japanese in Tokyo; Chinese in Beijing; Utah residents with ancestry from northern and western Europe; Luhya in Webuye, Kenya; Maasai in Kinyawa, Kenya; Toscani in Italy; Gujarati Indians in Houston; Chinese in metropolitan Denver; people of Mexican ancestry in Los Angeles; and people of African ancestry in the southwestern United States. The goal Project is to find most genetic variants that have frequencies of at least 1% in the populations studied. Sequencing is still too expensive to deeply sequence the many samples being studied for this project. However, any particular region of the genome generally contains a limited number of haplotypes. Data can be combined across many samples to allow efficient detection of most of the variants in a region. The Project currently plans to sequence each sample to about 4X coverage; at this depth sequencing cannot provide the complete genotype of each sample, but should allow the detection of most variants with frequencies as low as 1%. Combining the data from 2500 samples should allow highly accurate estimation (imputation) of the variants and genotypes for each sample that were not seen directly by the light sequencing. All samples from the 1000 genomes are available as lymphoblastoid cell lines (LCLs) and LCL derived DNA from the Coriell Cell Repository as part of the NHGRI Catalog. The sequence and alignment data generated by the 1000genomes project is made available as quickly as possible via their mirrored ftp sites. ftp://ftp.1000genomes.ebi.ac.uk ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes

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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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Cite this (1DegreeBio, RRID:SCR_011994)

URL: http://1degreebio.org/

Resource Type: Resource, software resource

A registry which provides links and reviews for material resources such as reagents, equipment, digital tools, and providers, as well as the companies that sell them. Users can search for specific materials or search by vendor, product, or service type.

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    3D Brain

Cite this (3D Brain, RRID:SCR_013138)

URL: https://itunes.apple.com/be/app/3d-brain/id331399332?mt=8

Resource Type: Resource, software application, narrative resource, training material, software resource, mobile app, data or information resource

iPhone and iPad app that provides a good overview of the brain and its structures allowing you to rotate and zoom around 29 interactive structures with your touch screen. Discover how each brain region functions, what happens when it is injured, and how it is involved in mental illness. Each detailed structure comes with information on functions, disorders, brain damage, case studies, and links to modern research. Compatible with iPhone, iPod touch and iPad. Requires iOS 3.0 or later.

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Cite this (3D de novo assembly, RRID:SCR_017227)

URL: https://github.com/theaidenlab/3d-dna.git

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

Software tool as 3D de novo assembly (3D DNA) pipeline. Used to help generate HI-C assembly.

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Cite this (3D Genome, RRID:SCR_017525)

URL: http://promoter.bx.psu.edu/hi-c/

Resource Type: Resource, service resource

Genome Browser for study of 3D genome organization and gene regulation and data visualization. Used to visualizing chromatin interaction data, browse other omics data such as ChIP-Seq or RNA-Seq for same genomic region, and gain complete view of both regulatory landscape and 3D genome structure for any given gene.

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Cite this (3D Objects Counter, RRID:SCR_017066)

URL: https://imagej.net/3D_Objects_Counter

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

Software tool as plugin for ImageJ. Counts the number of 3D objects in stack, quantifies for each found object, generates results representations.

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Cite this (3D Roi Manager, RRID:SCR_017065)

URL: http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_roi_manager:start

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

Software tool as plugin for ImageJ. Used for 3D objects and image can be segmented directly within plugin via 3D segment button.

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Cite this (4D Genome, RRID:SCR_017489)

URL: https://4dgenome.research.chop.edu/

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Repository for chromatin interaction data. Records can be queried by genomic regions, gene names, organism, and detection technology. Database is continuously updated by curators. Contributions from scientific community.

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    4Peaks

Cite this (4Peaks, RRID:SCR_000015)

URL: http://nucleobytes.com/index.php/4peaks

Resource Type: Resource, software resource, software application

Software application for viewing and editing sequence trace files.

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Cite this (60-Second Mind, RRID:SCR_000925)

URL: http://www.scientificamerican.com/podcast/60-second-mind/

Resource Type: Resource, narrative resource, data or information resource

A podcast of neuroscience news in minute-intervals from the Scientific American. New episodes become available every Saturday.

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    AAL

Cite this (AAL, RRID:SCR_003550)

URL: http://www.gin.cnrs.fr/spip.php?article216

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

Software for automated anatomical labeling of activations in SPM (Statistical Parametric Mapping) using a macroscopic anatomical parcellation of the MNI MRI single-subject brain. The software was used for an automated anatomical parcellation of the spatially normalized single-subject high-resolution T1 volume provided by the Montreal Neurological Institute (MNI) (D. L. Collins et al., 1998, Trans. Med. Imag. 17, 463468, PubMed). Using this parcellation method, three procedures to perform the automated anatomical labeling of functional studies were proposed: (1) labeling of an extremum defined by a set of coordinates, (2) percentage of voxels belonging to each of the anatomical volumes of interest (AVOI) intersected by a sphere centered by a set of coordinates, and (3) percentage of voxels belonging to each of the AVOI intersected by an activated cluster. An interface with the Statistical Parametric Mapping package is provided as a freeware to researchers of the neuroimaging community.

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    ABACAS

Cite this (ABACAS, RRID:SCR_015852)

URL: http://abacas.sourceforge.net

Resource Type: Resource, software resource, software application

Software that contiguates (align, order, orientate), visualizes and designs primers to close gaps on shotgun assembled contigs based on a reference sequence. ABACAS finds alignment positions and identifies syntenies of assembled contigs against the reference, then generates a pseudomolecule taking overlapping contigs and gaps into account.

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Cite this (ABA Mouse Brain: Atlas, RRID:SCR_017479)

URL: http://mouse.brain-map.org/

Resource Type: Resource, service resource, data or information resource, database

Genome wide database of gene expression in mouse brain.

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Cite this (ABC Bacterial Transporter Systems Database, RRID:SCR_016617)

URL: https://bioinformatics.niaid.nih.gov/abctransporter/

Resource Type: Resource, data or information resource, database

Collection of classified bacterial ATP-binding cassette (ABC) transporter systems. The transporter systems identified fulfill the three roles characterized by the nucleotide-binding domain (NBD) , transmembrane domain (TMD), and solute-binding protein (SBP) domains.

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Cite this (ABCDreport, RRID:SCR_016030)

URL: https://github.com/ABCD-STUDY/ABCDreport

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

Software application as a simple system to review study progress. Used in ABCD study.

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Cite this (AbsCN-seq, RRID:SCR_006409)

URL: http://bioinformatics.oxfordjournals.org/content/early/2014/01/02/bioinformatics.btt759.abstract?sid=e62f3c2b-26dc-428b-ba24-99e92a277d77

Resource Type: Resource, software resource

Statistical software to estimate tumor purity, ploidy and absolute copy numbers from next generation sequencing data.

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Cite this (ABSORB: Atlas Building by Self-Organized Registration and Bundling, RRID:SCR_007018)

URL: http://bric.unc.edu/ideagroup/free-softwares/ABSORB/

Resource Type: Resource, image analysis software, data processing software, source code, software application, software resource, registration software

This software package implements an algorithm for effective groupwise registration. The required input is a set of 3D MR intensity images (in Analyze format with paired .hdr and .img files) with a text file (.txt) listing all header file (.hdr) names. The output is the set of registered images together with the corresponding dense deformation fields. This software has been tested on Windows XP (32-bit) and Linux (64-bit, kernel version 2.6.18-194.el5). The images should be pre-processed before applying ABSORB: * All brain MR images used as inputs to ABSORB should be in the same situation (e.g., skull-stripped or not, cerebellum removed or not, etc.). * The input images should be in Analyze format with paired header and image files. This software was developed in IDEA group in UNC-Chapel Hill.

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Cite this (AbundanceBin, RRID:SCR_004648)

URL: http://omics.informatics.indiana.edu/AbundanceBin/

Resource Type: Resource, software resource

An abundance-based software tool for binning metagenomic sequences, such that the reads classified in a bin belong to species of identical or very similar abundances. AbundanceBin also gives estimations of species abundances and their genome sizes -two important characteristic parameters for a microbial community.

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