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

All-in-one computer program for robust and rapid analysis of quantitative reverse transcription real-time polymerase chain reaction (RT-qPCR) data in SAS. It incorporates all functions important for RT-qPCR data analysis including assessment of PCR efficiencies, validation of internal reference genes and normalizers, normalization of confounding variations across samples and statistical comparisons of target gene expression in parallel samples. The program is highly automatic in data analyses and result output. The input data have no limitations for the number of genes or cDNA samples. Users can simply change the macro variables to test various analytical strategies, optimize results and customize the analytical processes. The program is also extendable allowing advanced SAS users to develop particular statistical tests appropriate for their experimental designs. Thus users are the actual decision-makers controlling RT-qPCR data analyses. The program has to be used in SAS software; however, extensive SAS programming knowledge is not required.

Proper citation: SASqPCR (RRID:SCR_003056) Copy   

•   Source: SciCrunch Registry

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

R package providing functions to assess and to compare the performance of risk prediction (survival) models.

Proper citation: SurvComp (RRID:SCR_003054) Copy   

•   Source: SciCrunch Registry

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

Software that aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation).

Proper citation: Parametric Time Warping (RRID:SCR_003053) Copy   

•   Source: SciCrunch Registry

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

An interactive, user-editable genetic sequence database tool, targeted at molecular biology research groups that can be browsed using tags. The tool is Web 2.0-flavoured, allowing users to do more than just retrieve information. Its focus on user-editability is supported by the use of tags (metadata) associated with genetic sequences. Several methods of retrieving stored data are available including tag-clouds, BLAST and keyword searches. Also, sequence tags related to HGNC gene names, conserved domains (CDD) and GO terms can be automatically generated given sequence data. The tool is constructed using the high-level Python web framework, Django, with a SQLite3 backend.

Proper citation: Gutentag (RRID:SCR_003051) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/pacBioToCA

A module in the Celera Assembler software package that performs error correction on PacBio long reads by mapping shorter, high accuracy reads onto the long reads.

Proper citation: PacBioToCA (RRID:SCR_003044) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/R-pbutils

An R software package providing plotting and convenience functions.

Proper citation: R-pbutils (RRID:SCR_002995) Copy   

•   Source: SciCrunch Registry

http://www.dana-farber.org/

Cancer institute that provides expert, compassionate care to children and adults with cancer while advancing the understanding, diagnosis, treatment, cure, and prevention of cancer and related diseases. As an affiliate of Harvard Medical School and a Comprehensive Cancer Center designated by the National Cancer Institute, the Institute also provides training for new generations of physicians and scientists, designs programs that promote public health particularly among high-risk and underserved populations, and disseminates innovative patient therapies and scientific discoveries to their target community across the United States and throughout the world.

Proper citation: Dana-Farber Cancer Institute (RRID:SCR_003040) Copy   

•   Source: SciCrunch Registry

http://www.research.philips.com/

A global organization that helps Philips introduce innovations that improve people's lives by providing technology options for innovations in the area of health and well-being, targeted at both developed and emerging markets. Positioned at the front-end of the innovation process, they work on everything from spotting trends and ideation to proof of concept and - where needed - first-of-a-kind product development.

Proper citation: Philips Research (RRID:SCR_003871) Copy   

•   Source: SciCrunch Registry

http://roslincells.com/

Organization that supplies undifferentiated, clinical grade, human pluripotent stem cell lines to the life science community, and works with academic, clinical and commercial colleagues to enable and facilitate the use of these high grade cells in the development of new reagents, drugs and cellular therapeutics. They also seek to drive the economic development of the stem cell sector in Scotland. Their products can act as a valuable tool in supporting clients' drug discovery, development and clinical research programmes.

Proper citation: Roslin Cells (RRID:SCR_003857) Copy   

•   Source: SciCrunch Registry

http://www.exelixis-lab.org/software.html

Software for an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.

Proper citation: PEAR (RRID:SCR_003776) Copy   

•   Source: SciCrunch Registry

http://www.esi.com/

A high technology company that is a developer and supplier of photonic and laser systems for microelectronics manufacturers. They manufacture a variety of products for testing and repairing equipment, and particularly products designed for use by manufacturers of other high-tech products. These include laser trimming systems. (Adapted from Wikipedia)

Proper citation: Electro Scientific Industries (RRID:SCR_003895) Copy   

•   Source: SciCrunch Registry

http://www.iaeste.org/

An independent, non-profit and non-political student exchange organization that provides students in technical degrees (primarily Science, Engineering and the applied arts) with paid, course-related, training abroad and employers with highly skilled, highly motivated trainees, for long or short term projects.

Proper citation: IAESTE (RRID:SCR_003773) Copy   

•   Source: SciCrunch Registry

http://www.inserm-transfert.fr/en/

A private subsidiary of the French National Institute of the Health and Medical Research (Inserm), dedicated to technology transfer (from invention disclosure to industrial partnership). It manages European and International research projects, supports large scale projects in epidemiology and public health. It has run a proof of concept fund. The company is also committed to seed financing in the biotech sector, through its dedicated seed fund company Inserm Transfert Initiative. www.inserm-transfert.fr

Proper citation: Inserm Transfert (RRID:SCR_003808) Copy   

•   Source: SciCrunch Registry

http://www.chevron.com/

An American multinational energy corporation headquartered in San Ramon, California, and active in more than 180 countries, that is engaged in every aspect of the oil, gas, and geothermal energy industries, including exploration and production; refining, marketing and transport; chemicals manufacturing and sales; and power generation. Chevron is one of the world's largest oil companies; as of 2013, it ranked third in the Fortune Global 500-2014 list of the world's largest companies. (Adapted from Wikipedia)

Proper citation: Chevron Corporation (RRID:SCR_003794) Copy   

•   Source: SciCrunch Registry

http://www.bioreliance.com/

Company that provides testing and manufacturing services to pharmaceutical and biopharmaceutical companies that span the product cycle from early pre-clinical development to licensed production.

Proper citation: BioReliance (RRID:SCR_003791) Copy   

•   Source: SciCrunch Registry

http://www.selleckchem.com/

An Antibody supplier

Proper citation: Selleck Chemicals LLC (RRID:SCR_003823) Copy   

•   Source: SciCrunch Registry

http://www.bioclinica.com/

Pennsylvania-based company supporting pharmaceutical and medical device innovation with imaging core lab, EDC, IVR / IWR, CTMS, and supply chain forecasting and optimization. Its initial service was medical imaging for clinical trials. It is used to capture, collect, control quality, provide blinded reading services to the final delivery to the sponsor company and to the FDA or EMEA if required for medical images in a wide range of imaging modalities. (Wikipedia)

Proper citation: BioClinica (RRID:SCR_003789) Copy   

•   Source: SciCrunch Registry

http://www.musc.edu/

Public medical school in Charleston, South Carolina. Opened in 1824 as small private college aimed at training physicians. One of the oldest continually operating schools of medicine in the United States and the oldest in the Deep South.

Proper citation: Medical University of South Carolina; South Carolina; USA (RRID:SCR_003828) Copy   

•   Source: SciCrunch Registry

http://www.quretec.com/

Commercial organization that builds software for collection, management, and analysis of complex data, most typical in biomedical domain. The solutions are generic and can be used for multitude of uses and application domains.

Proper citation: Quretec (RRID:SCR_003826) Copy   

•   Source: SciCrunch Registry

http://www.onyx.com/

November 2020, Onyx merged with Legacy Acquisition Corp. to form PARTS iD, Inc. Our data intelligence, integrated platforms, product cataloging, digital marketing expertise, and virtual warehousing have ensured our continued leadership in the competitive marketplace.

Proper citation: Onyx Pharmaceuticals (RRID:SCR_003782) Copy   

•   Source: SciCrunch Registry