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http://neurolex.org/wiki/Main_Page

A freely editable semantic wiki for community-based curation of the terms used in Neuroscience. Entries are curated and eventually incorporated into the formal NIFSTD ontology. NeuroLex also includes a Resource branch for community members to freely add neuroscience relevant resources that do not become part of NIFSTD ontology but rather make up the NIF Registry. As part of the NIF, we provide a simple search interface to many different sources of neuroscience information and data. To make this search more effective, we are constructing ontologies to help organize neuroscience concepts into category hierarchies, e.g., neuron is a cell. These categories provide the means to perform more effective searches and also to organize and understand the information that is returned. But an important adjunct to this activity is to clearly define all of the terms that we use to describe our data, e.g., anatomical terms, techniques, organism names. Because wikis provide an easy interface for communities to contribute their knowledge, we started the NeuroLex.

Proper citation: NeuroLex (RRID:SCR_005402) Copy   

•   Source: SciCrunch Registry
  

http://neuinfo.org

Framework for identifying, locating, relating, accessing, integrating, and analyzing information from neuroscience research. Users can search for and add neuroscience-related resources at NIF portal and receive and RRID to track and cite resources within scientific manuscripts.

Proper citation: Neuroscience Information Framework (RRID:SCR_002894) Copy   

•   Source: SciCrunch Registry
  

http://ftp://lausanne.isb-sib.ch/pub/databases/Bgee/general/IQRray.R

Software based on evolutionary conservation of expression profiles, implemented in R, for identification of poor quality arrays in dataset composed of arrays from many independent experiments.

Proper citation: IQRray (RRID:SCR_006057) Copy   

•   Source: SciCrunch Registry
  

http://cran.r-project.org/web/packages/fcros/

A fold change ranks ordering statistics based software for detecting differentially expressed genes.

Proper citation: FCROS (RRID:SCR_006195) Copy   

•   Source: SciCrunch Registry
  

http://epigenomegateway.wustl.edu/

Software tool for visualizing and interacting with whole-genome datasets. Browser hosts Human Epigenome Atlas data produced by Roadmap Epigenomics project, but its use of advanced, multi-resolution data formats and its user-friendly interface make it possible for investigators to upload and visualize their own data as custom tracks. Developed and maintained by Epigenome Informatics Group at Washington University in St. Louis.

Proper citation: WashU Epigenome Browser (RRID:SCR_006208) Copy   

•   Source: SciCrunch Registry
  

http://isaac.bioapps.biozentrum.uni-wuerzburg.de/isaac/modules/genome/species.xhtml

Web based tool to enable the analysis of sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis. Detailed history and snapshot information allows tracing each action. One can switch back to previous states and perform new analyses. Sets can be viewed in the context of genomes, protein functions, protein interactions, pathways, regulation, diseases and drugs. Additionally, users can switch between species with an automatic, orthology based translation of existing gene sets. Sets as well as results of analyses can be exchanged between members of groups.

Proper citation: InterSpecies Analysing Application using Containers (RRID:SCR_006243) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/devel/bioc/html/RUVSeq.html

Software package that implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.

Proper citation: RUVSeq (RRID:SCR_006263) Copy   

•   Source: SciCrunch Registry
  

http://cran.r-project.org/web/packages/YuGene/

Software providing a simple method for comparison of gene expression generated across different experiments, and on different platforms; that does not require global renormalization, and is not restricted to comparison of identical probes. YuGene works on a range of microarray dataset distributions, such as between manufacturers. The resulting output allows direct comparisons of gene expression between experiments and experimental platforms.

Proper citation: YuGene (RRID:SCR_006023) Copy   

•   Source: SciCrunch Registry
  

http://dna.cs.byu.edu/gnumap/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. A probabilistic algorithm that addresses the computational problems associated with aligning bisulfite sequencing data to a reference genome.

Proper citation: GNUMAP-BS (RRID:SCR_005995) Copy   

•   Source: SciCrunch Registry
  

http://galaxyproject.org/

Open, web-based platform providing bioinformatics tools and services for data intensive genomic research. Platform may be used as a service or installed locally to perform, reproduce, and share complete analyses. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Community has created Galaxy instances in many different forms and for many different applications including Galaxy servers, cloud services that support Galaxy instances, and virtual machines and containers that can be easily deployed for your own server.The Galaxy team is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University.Training Infrastructure as a Service (TIaaS) is a service offered by some UseGalaxy servers to specifically support training use cases.

Proper citation: Galaxy (RRID:SCR_006281) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/2.14/bioc/html/h5vc.html

Software package that contains functions to interact with tally data from Next-Generation Sequencing (NGS) experiments that is stored in HDF5 files.

Proper citation: h5vc (RRID:SCR_006039) Copy   

•   Source: SciCrunch Registry
  

https://bitbucket.org/cob87icW6z/cafe/wiki/Home

R software package for the detection of gross chromosomal abnormalities from gene expression microarray data.

Proper citation: CAFE (RRID:SCR_005983) Copy   

•   Source: SciCrunch Registry
  

http://gensc.org/

An open-membership International community to promote mechanisms that standardize the description of genomes and the exchange and integration of genomic data. Community-driven standards have the best chance of success if developed within the auspices of international working groups. Participants in the GSC include biologists, computer scientists, those building genomic databases and conducting large-scale comparative genomic analyses, and those with experience of building community-based standards. The mission of the GSC is to work with the wider community towards: * the implementation of new genomic standards * methods of capturing and exchanging metadata * harmonization of metadata collection and analysis efforts across the wider genomics community

Proper citation: Genomic Standards Consortium (RRID:SCR_006273) Copy   

•   Source: SciCrunch Registry
  

http://www.megasoftware.net/mega-md/mega-md.php

Software to forecast the deleteriousness of non-synonymous single nucleotide variants (nsSNVs) using multiple methods and explore them in the context of the variability permitted in the long-term evolution of the affected positions. A web version (MEGA-MDW) is also available.

Proper citation: MEGA-MD (RRID:SCR_006403) Copy   

•   Source: SciCrunch Registry
  

http://www.uni-koeln.de/med-fak/cgars/

Software package to dissect random from non-random patterns in copy number data and thereby to assess significantly enriched somatic copy number aberrations (SCNA) across a set of tumor specimens or cell lines.

Proper citation: CGARS (RRID:SCR_006404) Copy   

•   Source: SciCrunch Registry
  

http://www2.warwick.ac.uk/fac/sci/systemsbiology/staff/ott/tools_and_software/wigwams

A computational tool for analyzing multiple gene expression time series data sets for the same organism. The goal is to determine if there is evidence for gene regulatory mechanisms that are shared by multiple different expression responses.

Proper citation: Wigwams (RRID:SCR_006400) Copy   

•   Source: SciCrunch Registry
  

http://www.unc.edu/~yunmli/betaseq/

Software to control Type-I error inflation in partially sequenced data for rare variant association testing. It is typically used to combine sequence and genotype data for the two stage design, in which individuals sequenced in stage one for variant detection are solely or predominantly cases then in stage two the discovered variants are genotyped in the remaining individuals. BETASEQ can work with any existing rare variant association methods that use genotypes or imputed genotypes as input.

Proper citation: BETASEQ (RRID:SCR_006401) Copy   

•   Source: SciCrunch Registry
  

https://code.google.com/p/saap-rrbs/

Streamlined Analysis and Annotation Pipeline for reduced representation bisulfite sequencing.

Proper citation: SAAP-RRBS (RRID:SCR_006516) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/ena/

Public archive providing a comprehensive record of the world''''s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. All submitted data, once public, will be exchanged with the NCBI and DDBJ as part of the INSDC data exchange agreement. The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources including submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centers and routine and comprehensive exchange with their partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature. ENA is made up of a number of distinct databases that includes the EMBL Nucleotide Sequence Database (Embl-Bank), the newly established Sequence Read Archive (SRA) and the Trace Archive. The main tool for downloading ENA data is the ENA Browser, which is available through REST URLs for easy programmatic use. All ENA data are available through the ENA Browser. Note: EMBL Nucleotide Sequence Database (EMBL-Bank) is entirely included within this resource.

Proper citation: European Nucleotide Archive (ENA) (RRID:SCR_006515) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/IRanges/

Software tool for computing and annotating genomic ranges.Provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent Vector API as much as possible.

Proper citation: IRanges (RRID:SCR_006420) Copy   

•   Source: SciCrunch Registry