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http://www.clinfowiki.org/wiki/index.php/Main_Page

A Wiki devoted to topics in clinical informatics. Contents: 1 Health Information Technology Regional Extension Centers 2 Free and Open Source Software (FOSS) licensing in medicine 3 Electronic Healthcare Communication 4 Electronic Medical Record (EMR) Systems 5 Computer-based Provider Order Entry -- CPOE 6 Clinical Decision Support -- CDS 7 Books on Topics in Clinical Informatics 8 Medical Devices, Computerized -- SmartDevices 9 Personal Health Records -- PHRs 10 Personal Health Applications -- PHAs 11 Informatics Students'' Contributions 12 Blueprint for a Comprehensive HIT System 13 Biobanking -- a.k.a. Biorepositories or Tissue Banks 14 Organizational issues 15 Regional Health Information Organizations -- RHIOs 16 Evidence-Based Medicine -- EBM 17 Evaluation Methods in Informatics 18 Unintended Consequences of Health Information Technology 19 Quality & Quality Informatics 20 Public Health Informatics 21 U.S. Federal Health Information Technology Initiatives 22 The E-Patient-Provider Relationship 23 Interface Terminology 24 New CIS-related Technologies 25 Workflow 26 Terminology and Coding 27 Interface/Usability Testing 28 International views 29 Blogposium, April 2006 30 Departments / Schools of Biomedical or Medical Informatics 31 Endowed Professorships and Chairs in Health / Medical / Nursing / Biomedical Informatics 32 Leading Health Informatics and Medical Informatics Journals o 32.1 Ranking of ISI/SCI listed e-Health and Medical Informatics Journals o 32.2 Not listed / ranked in ISI/SCI 33 External Links 34 External Medical Reference Links 35 External Informatics Organizations Links

Proper citation: Clinical Informatics Wiki (RRID:SCR_010518) Copy   

•   Source: SciCrunch Registry

https://medschool.ucsd.edu/Pages/default.aspx

Graduate medical school of University of California, San Diego. It was the third medical school in the University of California system, after those established at UCSF and UCLA, and is the only medical school in the San Diego metropolitan area.

Proper citation: University of California San Diego School of Medicine; California; USA (RRID:SCR_010634) Copy   

•   Source: SciCrunch Registry

http://www.abbvie.com/

A research-based biopharmaceutical company that develops advanced therapies to address global health problems.

Proper citation: AbbVie (RRID:SCR_010484) Copy   

•   Source: SciCrunch Registry

http://www.cff.org/

The mission of the Cystic Fibrosis Foundation, a nonprofit donor-supported organization, is to assure the development of the means to cure and control cystic fibrosis and to improve the quality of life for those with the disease. The Foundation is the leading organization in the United States devoted to cystic fibrosis. It funds and accredits more than 115 CF care centers, 95 adult care programs and 50 affiliate programs, and more than 75 chapters and branch offices nationwide. The Cystic Fibrosis Foundation is one of the most efficient organizations of its kind and is an accredited charity of the Better Business Bureau''s Wise Giving Alliance. Until we conquer this disease, our team will work tirelessly to extend and enhance life for those with cystic fibrosis by functioning as: * Scientific pioneers, blazing new trails in CF research; * Fund-raisers, securing the money needed to support our efforts; * Advocates, keeping CF a top priority in government, industry and research; * Investors, funding drug discovery and development; * Caregivers, linking patients and families to specialized CF care; and * Family, offering support, information and resources.

Proper citation: Cystic Fibrosis Foundation (RRID:SCR_010726) Copy   

•   Source: SciCrunch Registry

http://wanglab.pcbi.upenn.edu/coral/

A machine learning software package that can predict the precursor class of small RNAs present in a high-throughput RNA-sequencing dataset. In addition to classification, it also produces information about the features that are most important for discriminating different populations of small non-coding RNAs.

Proper citation: CoRAL - Classification of RNAs by Analysis of Length (RRID:SCR_010828) Copy   

•   Source: SciCrunch Registry

http://paed.hku.hk/uploadarea/yangwl/html/software.html

A toolkit for prioritizing SNVs and indels from next-generation sequencing data.

Proper citation: PriVar (RRID:SCR_010784) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.toronto.edu/CNVer/

A method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation.

Proper citation: CNVer (RRID:SCR_010820) Copy   

•   Source: SciCrunch Registry

http://sv.gersteinlab.org/cnvnator/

An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.

Proper citation: CNVnator (RRID:SCR_010821) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/diplotyper/

A fully automated software tool which is available for Linux to investigate associations between a diplotype group and a phenotype in linear or logistic regression.

Proper citation: Diplotyper (RRID:SCR_010789) Copy   

•   Source: SciCrunch Registry

http://bioinfo-out.curie.fr/projects/freec/tutorial.html

Prediction of copy number alterations and loss of heterozygosity using deep-sequencing data.

Proper citation: Control-FREEC (RRID:SCR_010822) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/readdepth/

This package for R can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome.

Proper citation: readDepth (RRID:SCR_010824) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/vibansal/software/hapcut

A max-cut based algorithm for haplotype assembly using sequence reads from the two chromosomes of an individual.

Proper citation: HapCUT (RRID:SCR_010791) Copy   

•   Source: SciCrunch Registry

http://www.popgen.dk/software/index.php/Relate

Software providing a method that estimates the probability of sharing alleles identity by descent (IBD) across the genome and can also be used for mapping disease loci using distantly related individuals.

Proper citation: Relate (RRID:SCR_010794) Copy   

•   Source: SciCrunch Registry

http://www.nig.ac.jp/index-e.html

Institute for genetics, through National BioResource Project, collects, preserves, and provides bio-resources (strains, populations, tissues, cells, genes of animals, plants and microorganisms, and information on these materials for R&D use) that are essential for life science research.

Proper citation: National Institute of Genetics; Shizuoka; Japan (RRID:SCR_010836) Copy   

•   Source: SciCrunch Registry

http://mirexpress.mbc.nctu.edu.tw/

A stand-alone software package implemented for generating miRNA expression profiles from high-throughput sequencing of RNA without the need for sequenced genomes.

Proper citation: miRExpress (RRID:SCR_010831) Copy   

•   Source: SciCrunch Registry

http://hugeseq.snyderlab.org/

An automated pipeline for detecting genetic variants from High-throUghput GEnome SEQuencing.

Proper citation: HugeSeq (RRID:SCR_010803) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/mutfinder/

It streamlines the next generation sequencing data analysis using BFAST for aligner, SAMTOOLS for SNP caller, and ANNOVAR for annotation.

Proper citation: MutFinder (RRID:SCR_010804) Copy   

•   Source: SciCrunch Registry

http://icbi.at/software/simplex/simplex.shtml

Cloud-enabled pipeline for the comprehensive analysis of exome sequencing data.

Proper citation: SIMPLEX (RRID:SCR_010807) Copy   

•   Source: SciCrunch Registry

http://epigen.hpc.cineca.it/wep/

A complete whole-exome sequencing pipeline and provides easy access through interface to intermediate and final results.

Proper citation: WEP (RRID:SCR_010809) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.toronto.edu/modil/

Software for a novel method for finding medium sized indels from high throughput sequencing datasets.

Proper citation: MoDIL (RRID:SCR_010764) Copy   

•   Source: SciCrunch Registry