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Public university for graduate education, under the direct leadership of the Chinese Academy of Sciences.
Proper citation: Chinese Academy of Sciences; Beijing; China (RRID:SCR_012797) Copy
Executive branch department of the federal government charged with coordinating and supervising all agencies and functions of the government directly related to national security and the United States Armed Forces.
Proper citation: U.S. Department of Defense (RRID:SCR_012712) Copy
Providing quality resources for the management of cerebral aneurysms and features an online calculator that calculates cerebral aneurysm volume and percent packing volume after coil embolization. The site also host an imaging Library with neuroanatomy and neurovascular images.
Proper citation: AngioCalc Cerebral Aneurysm Calculator (RRID:SCR_012805) Copy
http://umcd.humanconnectomeproject.org
Web-based repository and analysis site for connectivity matrices that have been derived from neuroimaging data including different imaging modalities, subject groups, and studies. Users can analyze connectivity matrices that have been shared publicly and upload their own matrices to share or analyze privately.
Proper citation: USC Multimodal Connectivity Database (RRID:SCR_012809) Copy
Unix-like operating system that is free software. GNU (more precisely, GNU/Linux systems) are entirely free software. The GNU Project was launched in 1984 to develop the GNU system. A Unix-like operating system is a software collection of applications, libraries, and developer tools, plus a program to allocate resources and talk to the hardware, known as a kernel. The Hurd, GNU''s own kernel, is some way from being ready for daily use. Thus, GNU is typically used today with a kernel called Linux. This combination is the GNU/Linux operating system. GNU/Linux is used by millions, though many call it Linux by mistake.
Proper citation: GNU.org (RRID:SCR_012764) Copy
http://bioconductor.org/packages/edgeR/
Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.
Proper citation: edgeR (RRID:SCR_012802) Copy
http://tare.medisin.ntnu.no/motiflab/
Software for a general workbench for analyzing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules.
Proper citation: MotifLab (RRID:SCR_012649) Copy
http://ciliate.org/index.php/home/welcome
TGD Wiki is a user-updatable database of information about the Tetrahymena thermophila genome sequence determined at The Institute for Genomic Research (TIGR). TGD Wiki provides information on the genome, genes, and proteins of Tetrahymena collected from the scientific literature, research community and many other resources. In order to keep the information in our database as current as possible, we will soon be inviting the members of the Tetrahymena community to add and update these annotations to reflect published research. TGD Wiki currently offers the following features: * Free, unrestricted read access to all available data * Sequence and annotation data for 24,725 genes (TIGR v.2008) * GBrowse genome browser with links to and from each gene page (TIGR v.2006) * BLAST searching of the TIGR gene models and genome sequence (TIGR v.2006) Tetrahymena Genome Database (TGD) Wiki began in 2004 at Stanford University using the schema and programs of its parent project, Saccharomyces Genome Database. TGD Wiki is now a collaboration between Bradley University, Stanford University, and Cornell University. As we begin TGD Wiki at its new home at Bradley University, the TGD Wiki database contains the following data from TGD: * Gene Names and Aliases * Gene Descriptions * Gene Ontology (GO) Annotations * Homologs (similar genes in selected organisms) * Protein Domains * Associated Literature * Paragraphs (longer, free-text descriptions of gene function, structure, and significance) * Coding and Protein Sequences We have updated the following fields to match the newest gene model sequences (TIGR v.2008): Coding and Protein Sequences, Protein Domains and Gene Descriptions. We will also be recalculating the GO Annotations (IEA evidence code) and Homologs as part of our effort to keep the annotations in TGD Wiki as current as possible. We will be relying on members of the Tetrahymena community to maintain high-quality, updated annotations in the remainder of the fields using our annotation interface. Also setting up new database superdb - for unpublished data Look at Ciliate.org for news on this and other new databases
Proper citation: TGD (RRID:SCR_012803) Copy
Integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.
Proper citation: KEGG (RRID:SCR_012773) Copy
http://www.bioconductor.org/packages/release/bioc/html/tRanslatome.html
Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions among different levels of gene expression, using several statistical methods: Rank Product, t-test, SAM, Limma, ANOTA, DESeq, edgeR.
Proper citation: tRanslatome (RRID:SCR_012810) Copy
A high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates, serving as the global reference in immunogenetics and immunoinformatics. IMGT provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools.
Proper citation: IMGT - the international ImMunoGeneTics information system (RRID:SCR_012780) Copy
http://sourceforge.net/p/krona/home/krona/
Software that allows hierarchical data to be explored with zoomable pie charts.
Proper citation: Krona (RRID:SCR_012785) Copy
Independent agency of the U.S. federal government that administers Social Security, a social insurance program consisting of retirement, disability, and survivor benefits.
Proper citation: U.S. Social Security Administration (RRID:SCR_012905) Copy
https://github.com/bedops/bedops
A suite of tools to address common questions raised in genomic studies - mostly with regard to overlap and proximity relationships between data sets.
Proper citation: BEDOPS (RRID:SCR_012865) Copy
http://www2.hu-berlin.de/eyetracking-eeg
A plugin for the open-source MATLAB toolbox EEGLAB developed with the goal to facilitate integrated analyses of electrophysiological and oculomotor data. The plugin parses, imports, and synchronizes simultaneously recorded eye tracking data and adds it as extra channels to the EEG. Saccades and fixations can be imported from the eye tracking raw data or detected with an adaptive velocity-based algorithm. Eye movements are then added as new time-locking events to EEGLAB's event structure, allowing easy saccade- and fixation-related EEG analysis (e.g., fixation-related potentials, FRPs). Alternatively, EEG data can be aligned to stimulus onsets and analyzed according to oculomotor behavior (e.g. pupil size, microsaccades) in a given trial. Saccade-related ICA components can be objectively identified based on their covariance with the electrically independent eye tracker. All functions can be accessed via EEGLAB's GUI or called from the command line.
Proper citation: EYE-EEG (combined eye-tracking & EEG) (RRID:SCR_012903) Copy
http://genome.dkfz-heidelberg.de/cgi-bin/GENSCAN/genscan.cgi
Resource out of service. Documented on February 24,2021.
Proper citation: GENSCAN (RRID:SCR_012902) Copy
http://gmod.org/wiki/Flash_GViewer
Flash GViewer is a customizable Flash movie that can be easily inserted into a web page to display each chromosome in a genome along with the locations of individual features on the chromosomes. It is intended to provide an overview of the genomic locations of a specific set of features - eg. genes and QTLs associated with a specific phenotype, etc. rather than as a way to view all features on the genome. The features can hyperlink out to a detail page to enable to GViewer to be used as a navigation tool. In addition the bands on the chromosomes can link to defineable URL and new region selection sliders can be used to select a specific chromosome region and then link out to a genome browser for higher resolution information. Genome maps for Rat, Mouse, Human and C. elegans are provided but other genome maps can be easily created. Annotation data can be provided as static text files or produced as XML via server scripts. This tool is not GO-specific, but was built for the purpose of viewing GO annotation data. Platform: Online tool
Proper citation: Flash Gviewer (RRID:SCR_012870) Copy
Public research university in Carbondale, Illinois. Founded in 1869, SIU is the oldest campus of the Southern Illinois University system.
Proper citation: Southern Illinois University; Illinois; USA (RRID:SCR_012873) Copy
http://bioconductor.org/help/mailing-list/
This mailing list is for announcements about Bioconductor and the availability of new code and questions and answers about problems and solutions using Bioconductor.
Proper citation: Bioconductor mailing list (RRID:SCR_012915) Copy
https://www.ncbi.nlm.nih.gov/assembly
Database providing information on structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data. The Archive links the raw sequence information found in the Trace Archive with assembly information found in publicly available sequence repositories (GenBank/EMBL/DDBJ).
Proper citation: NCBI Assembly Archive Viewer (RRID:SCR_012917) Copy
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