Tools   Select Another Resource Report Type

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

https://www.niddk.nih.gov/

Center with mission to conduct and support medical research and research training and to disseminate science-based information on diabetes and other endocrine and metabolic diseases. The NIDDK supports a wide range of medical research through grants to universities and other medical research institutions across the country.

Proper citation: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases (RRID:SCR_012895) Copy   

•   Source: SciCrunch Registry

https://github.com/BRAINSia/BRAINSTools

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. A graphical program to trace anatomical features in 3D image volumes. This tools is built upon the NA-MIC toolkit. The tool is fully compatible with Slicer3, and integrates the Slicer3 theme.

Proper citation: BRAINSTracer (RRID:SCR_012894) Copy   

•   Source: SciCrunch Registry

http://www.nsf.gov/

An independent federal agency created by Congress to promote the progress of science; to advance the national health, prosperity, and welfare; to secure the national defense They are the funding source for approximately 20 percent of all federally supported basic research conducted by America''s colleges and universities. In many fields such as mathematics, computer science and the social sciences, NSF is the major source of federal backing. NSF leadership has two major components: a director who oversees NSF staff and management responsible for program creation and administration, merit review, planning, budget and day-to-day operations; and a 24-member National Science Board (NSB) of eminent individuals that meets six times a year to establish the overall policies of the foundation.The director and all Board members serve six year terms. Each of them, as well as the NSF deputy director, is appointed by the President of the United States and confirmed by the U.S. Senate. At present, NSF has a total workforce of about 2,100 at its Arlington, Va., headquarters, including approximately 1,400 career employees, 200 scientists from research institutions on temporary duty, 450 contract workers and the staff of the NSB office and the Office of the Inspector General. NSF is the only federal agency whose mission includes support for all fields of fundamental science and engineering, except for medical sciences. They are tasked with keeping the United States at the leading edge of discovery in areas from astronomy to geology to zoology. So, in addition to funding research in the traditional academic areas, the agency also supports high-risk, high pay-off ideas, novel collaborations and numerous projects that may seem like science fiction today, but which the public will take for granted tomorrow. And in every case, they ensure that research is fully integrated with education so that today''s revolutionary work will also be training tomorrow''s top scientists and engineers NSF''s task of identifying and funding work at the frontiers of science and engineering is not a top-down process.

Proper citation: National Science Foundation (RRID:SCR_012938) Copy   

•   Source: SciCrunch Registry

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

A R package that enables the identification of protein binding footprints in DNase I hypersensitive sites sequencing (DNase-seq) data.

Proper citation: DNaseR (RRID:SCR_012819) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/acaciaerrorcorr/?source=navbar

Accurate error-correction of amplicon pyrosequences.

Proper citation: Acacia (RRID:SCR_012896) Copy   

•   Source: SciCrunch Registry

http://www.abcam.com

A commercial antibody supplier which supplies primary and secondary antibodies, biochemicals, proteins, peptides, lysates, immunoassays and other kits.

Proper citation: Abcam (RRID:SCR_012931) Copy   

•   Source: SciCrunch Registry

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

Software to infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores.

Proper citation: TargetScore (RRID:SCR_012933) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/oncosnp/

An analytical software tool for characterizing copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from SNP genotyping data.

Proper citation: OncoSNP (RRID:SCR_012985) Copy   

•   Source: SciCrunch Registry

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

A Genotype Calling Algorithm for Affymetrix SNP Arrays.

Proper citation: RLMM (RRID:SCR_012984) Copy   

•   Source: SciCrunch Registry

http://www.zebrafinchatlas.org

Expression atlas of in situ hybridization images from large collection of genes expressed in brain of adult male zebra finches. Goal of ZEBrA project is to develop publicly available on-line digital atlas that documents expression of large collection of genes within brain of adult male zebra finches.

Proper citation: Zebra Finch Expression Brain Atlas (RRID:SCR_012988) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ibdld/

A C++ software program for multipoint IBD estimation based on high density SNP genotype data.

Proper citation: IBDLD (RRID:SCR_013043) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/solsnp/

A Java-based DNA variant calling tool for Next-Generation Sequencing alignment data.

Proper citation: SolSNP (RRID:SCR_013045) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/tumorhats/

A software tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data.

Proper citation: HATS (RRID:SCR_013044) Copy   

•   Source: SciCrunch Registry

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

Software package that implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol.

Proper citation: charm (RRID:SCR_012992) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/chipotle-perl/

A peak-finding algorithm used to analyze ChIP-chip microarray data.

Proper citation: ChIPOTle Peak Finder (RRID:SCR_012991) Copy   

•   Source: SciCrunch Registry

http://rnaseq-mats.sourceforge.net/

Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user defined threshold. Can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design.

Proper citation: Multivariate Analysis of Transcript Splicing (RRID:SCR_013049) Copy   

•   Source: SciCrunch Registry

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

Software package that provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data.

Proper citation: BiSeq (RRID:SCR_012993) Copy   

•   Source: SciCrunch Registry

http://trinityrnaseq.sourceforge.net/

Software for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.

Proper citation: Trinity (RRID:SCR_013048) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngspeanalysis/

A pipeline using open-source tools which can implement a set of pair ended Next-generation sequencing analysis, include short reads alignment, high-quality variation genotype calling and variants annotation.

Proper citation: NGSpeAnalysis (RRID:SCR_013040) Copy   

•   Source: SciCrunch Registry