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http://www.nbic.nl/

A collaborative institute of the bioinformatics groups in the Netherlands that perform cutting-edge research, develop novel tools and support platforms, create an e-science infrastructure and educate the next generations of bioinformaticians. They aim to build and maintain a strong bioinformatics and e-bioscience community that meets the (growing) demand for bioinformatics expertise, infrastructure and personnel in the Dutch life sciences field and provides a stimulating force for advanced research in biology. The NBIC grants aim to support the NBIC projects and (the visibility of) the NBIC community. Therefore, only people working in NBIC partner organizations can apply for sponsoring by NBIC. Positions for postdocs and others are available and there is a yearly conference.

Proper citation: Netherlands Bioinformatics Centre (RRID:SCR_012879) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/BicARE.html

Biclustering Analysis and Results Exploration.

Proper citation: BicARE (RRID:SCR_012881) Copy   

•   Source: SciCrunch Registry

http://www.energy.gov/

The mission of the Department of Energy is to ensure America''s security and prosperity by addressing its energy, environmental, and nuclear challenges through transformative science and technology solutions. Goal 1: Transform our Energy Systems - Catalyze the timely, material, and efficient transformation of the nation''s energy system and secure U.S. leadership in clean energy technologies. Goal 2: The Science and Engineering Enterprise - Maintain a vibrant U.S. effort in science and engineering as a cornerstone of our economic prosperity, with clear leadership in strategic areas. Goal 3: Secure Our Nation - Enhance nuclear security through defense, nonproliferation, and environmental efforts. Goal 4: Management and Operational Excellence - Establish an operational and adaptable framework that combines the best wisdom of all Department stakeholders to maximize mission success.

Proper citation: United States Department of Energy (RRID:SCR_012841) Copy   

•   Source: SciCrunch Registry

http://www.usaid.gov/

Proper citation: USAID (RRID:SCR_012846) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/charm.html

Function for differentially methylated regions (DMR) detection that is a part of the charm package in R/Bioconductor.

Proper citation: dmrFinder (RRID:SCR_012853) Copy   

•   Source: SciCrunch Registry

https://darlinglab.org/mauve/mauve.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software as system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.

Proper citation: Mauve (RRID:SCR_012852) Copy   

•   Source: SciCrunch Registry

http://www.djangoproject.com/

Django is a high-level Python Web framework that encourages rapid development and clean, pragmatic design. Developed four years ago by a fast-moving online-news operation, Django was designed to handle two challenges: the intensive deadlines of a newsroom and the stringent requirements of the experienced Web developers who wrote it. It lets you build high-performing, elegant Web applications quickly. Django focuses on automating as much as possible and adhering to the DRY principle.

Proper citation: Django (RRID:SCR_012855) Copy   

•   Source: SciCrunch Registry

http://www.nidcd.nih.gov/

The National Institute on Deafness and Other Communication Disorders (NIDCD) is one of the Institutes that comprise the National Institutes of Health (NIH). Established in 1988, NIDCD is mandated to conduct and support biomedical and behavioral research and research training in the normal and disordered processes of hearing, balance, smell, taste, voice, speech, and language. The Institute also conducts and supports research and research training related to disease prevention and health promotion; addresses special biomedical and behavioral problems associated with people who have communication impairments or disorders; and supports efforts to create devices which substitute for lost and impaired sensory and communication function. It is estimated that more than 46 million people in the United States suffer some form of disordered communication. NIDCD has focused national attention on disorders of human communication and has contributed to advances in biomedical and behavioral research that will improve the lives of millions of individuals with communication disorders. NIDCD has made important contributions to the body of knowledge needed to help those who experience communication disorders and to advance research in all aspects of human communication. NIDCD accomplishes its mandate through the Division of Intramural Research, which conducts research in laboratories at the NIH, and the Extramural Research Program, a program of research grants, career development awards, individual and institutional research training awards, center grants, and contracts to public and private research institutions and organizations. As a whole, the Institute supports and conducts approximately 600 research projects. The Institute also conducts and supports research and research training in disease prevention and health promotion and the special biomedical and behavioral problems associated with people having communication impairments and disorders. NIDCD''s extramural grant portfolio demonstrates a balance of basic and clinical research. The intramural research program spans a variety of topics, including, but not limited to, the development of a vaccine against otitis media, the identification and characterization of genes responsible for hereditary hearing impairment, genes associated with neoplasms affecting human communication, and treatment of voice disorders.

Proper citation: National Institute on Deafness and Other Communication Disorders (RRID:SCR_012859) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html

Software package that includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements.

Proper citation: ChIPpeakAnno (RRID:SCR_012828) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/inSilicoMerging.html

Collection of techniques to remove inter-study bias when combining gene expression data originating from different studies.

Proper citation: inSilicoMerging (RRID:SCR_012829) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/DEXSeq.html

Software package focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.

Proper citation: DEXSeq (RRID:SCR_012823) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/snapCGH.html

Software providing methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays.

Proper citation: snapCGH (RRID:SCR_012947) Copy   

•   Source: SciCrunch Registry

http://www.fda.gov/ScienceResearch/BioinformaticsTools/Arraytrack/default.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. Provides an integrated solution for managing, analyzing, and interpreting microarray gene expression data.

Proper citation: ArrayTrack (RRID:SCR_012839) Copy   

•   Source: SciCrunch Registry

http://www.cihr-irsc.gc.ca/e/193.html

The Canadian Institutes of Health Research (CIHR) is the Government of Canada''s agency responsible for funding health research in Canada. CIHR was created in 2000 under the authority of the CIHR Act and reports to Parliament through the Minister of Health. CIHR''s budget for 2008-09 is $928.6 million, of which $132 million is allocated to administering the Networks of Centres of Excellence and Canada Research Chair programs. CIHR was created to transform health research in Canada by: * funding more research on targeted priority areas; * building research capacity in under-developed areas such as population health and health services research; * training the next generation of health researchers; and * focusing on knowledge translation, so that the results of research are transformed into policies, practices, procedures, products and services. CIHR consists of 13 virtual institutes, a structure that is unique in the world. These innovative institutes bring together all partners in the research process - the people who fund research, those who carry it out and those who use its results - to share ideas and focus on what Canadians need: good health and the means to prevent disease and fight it when it happens. Each institute supports a broad spectrum of research in its topic areas and, in consultation with its stakeholders, sets priorities for research in those areas.

Proper citation: Canadian Institutes of Health Research (RRID:SCR_012838) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/miRNApath.html

Software package that provides pathway enrichment techniques for miRNA expression data.

Proper citation: miRNApath (RRID:SCR_012833) Copy   

•   Source: SciCrunch Registry

http://repeatmasker.org/

Software tool that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher. RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library ) and RepBase ( consensus sequence library ).

Proper citation: RepeatMasker (RRID:SCR_012954) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/sva.html

Contains functions for removing batch effects and other unwanted variation in high-throughput experiment.

Proper citation: sva package (RRID:SCR_012836) Copy   

•   Source: SciCrunch Registry

http://www.csrees.usda.gov/

Proper citation: USDA National Institute of Food and Agriculture (RRID:SCR_012886) Copy   

•   Source: SciCrunch Registry

http://www.nigms.nih.gov/

NIGMS supports basic biomedical research that is not targeted to specific diseases. NIGMS funds studies on genes, proteins, and cells, as well as on fundamental processes like communication within and between cells, how our bodies use energy, and how we respond to medicines. The results of this research increase our understanding of life and lay the foundation for advances in disease diagnosis, treatment, and prevention. NIGMS also supports research training programs that produce the next generation of biomedical scientists, and it has special programs to encourage underrepresented minorities to pursue biomedical research careers. The National Institute of General Medical Sciences (NIGMS) primarily supports research that lays the foundation for advances in disease diagnosis, treatment, and prevention. The Institute's research training programs help provide the next generation of scientists. Each year, NIGMS-supported scientists make many advances in understanding fundamental life processes. In the course of answering basic research questions, these investigators increase our knowledge about the mechanisms and pathways involved in certain diseases. Institute grantees also develop important new tools and techniques, some of which have medical applications. In recognition of the significance of their work, a number of NIGMS grantees have received the Nobel Prize and other high scientific honors. At any given time, NIGMS supports approximately 4,700 research grants—approximately 11 percent of the grants funded by NIH as a whole. NIGMS also supports approximately 26 percent of the trainees who receive assistance from NIH. NIGMS also supports approximately 25% of the trainees who receive assistance from NIH. The Institute places great emphasis on supporting investigator-initiated research grants. It funds a limited number of research center grants in selected fields, including structural genomics, trauma and burn research, and systems biology. In addition, NIGMS supports several important scientific resources, including the NIGMS Human Genetic Cell Repository and the Protein Data Bank.

Proper citation: National Institute of General Medical Sciences (RRID:SCR_012887) Copy   

•   Source: SciCrunch Registry

http://www.ncl.ac.uk/

UK public research university based in Newcastle upon Tyne, North East England with overseas campuses in Singapore and Malaysia. The university is a red brick university and a member of the Russell Group, an association of research-intensive UK universities.

Proper citation: Newcastle University; Newcastle upon Tyne; United Kingdom (RRID:SCR_012923) Copy   

•   Source: SciCrunch Registry