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

Software package that carries out association analysis of common copy number variants in population-based studies. It includes functions for analysing association under a series of study designs (case-control, cohort, etc), using several dependent variables (class status, censored data, counts) as response, adjusting for covariates and considering various inheritance models. It also includes functions for inferring copy number (CNV genotype calling). Various classes and methods for generic functions (print, summary, plot, anova, ... ) have been created to facilitate the analysis.

Proper citation: CNVassoc (RRID:SCR_002901) Copy   

•   Source: SciCrunch Registry

http://colorado.edu/

Public university that offers degrees in the sciences, humanities, and social sciences.

Proper citation: University of Colorado Boulder; Colorado; USA (RRID:SCR_003114) Copy   

•   Source: SciCrunch Registry

http://chiulab.ucsf.edu/surpi/

Software providing a computational pipeline for pathogen identification from complex metagenomic next-generation sequencing (NGS) data generated from clinical samples.

Proper citation: SURPI (RRID:SCR_003071) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/fas-dpd/

Software program to design degenerate primers for PCR.

Proper citation: FAS-DPD (RRID:SCR_003068) Copy   

•   Source: SciCrunch Registry

http://pfind.ict.ac.cn/software/pFind/index.html

A search engine system for automated peptide and protein identification from tandem mass spectra.

Proper citation: pFind (RRID:SCR_003011) Copy   

•   Source: SciCrunch Registry

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

GAP is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, classic twin models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates.

Proper citation: Genetic Analysis Package (RRID:SCR_003006) Copy   

•   Source: SciCrunch Registry

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

Software for differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions.

Proper citation: tweeDEseq (RRID:SCR_003038) Copy   

•   Source: SciCrunch Registry

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

Software function that calculates the isotopic pattern (fine structures) for a given chemical formula.

Proper citation: Isopat (RRID:SCR_003025) Copy   

•   Source: SciCrunch Registry

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

Software package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S).

Proper citation: BRAIN (RRID:SCR_003018) Copy   

•   Source: SciCrunch Registry

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.feinberg.northwestern.edu/

Medical school of Northwestern University which focuses on research initiatives, clinical affiliates, and global outlook.

Proper citation: Northwestern University Feinberg School of Medicine; Illinois; USA (RRID:SCR_001058) Copy   

•   Source: SciCrunch Registry

http://www.princeton.edu/

A private Ivy League research university based in New Jersey that confers undergraduate and graduate degrees in the humanities, social sciences, natural sciences, and engineering. It offers professional degrees in international affairs, engineering and applied science, architecture, and finance

Proper citation: Princeton University; New Jersey; USA (RRID:SCR_001059) Copy   

•   Source: SciCrunch Registry

http://www.medicine.uic.edu/

The medical school division of the University of Illinois with four separate campuses. The school focuses on excellence in research, education and clinical work, diversity and innovation, and collaboration.

Proper citation: University of Illinois College of Medicine; Illinois; USA (RRID:SCR_001057) Copy   

•   Source: SciCrunch Registry

http://www.essentialtremor.org

The IETF is an international nonprofit organization whose mission is to provide global educational information, services and support to those affected by essential tremor (ET) and to health care providers, while promoting and funding ET research. Services provided by the IETF include mailing or emailing a free information packet about ET upon request, maintaining an up-to-date listing of physicians specializing in ET, and assisting in forming and maintaining ET support groups. In addition, the IETF conducts several free educational events in cities across the United States every year, and an annual awareness campaign that runs in conjunction with the organization's largest fundraising activity, Tulips for Tremors. Every year, the IETF also funds basic research into the cause(s) of ET. Small grants are awarded to established scientists whose primary interest is tremor disorders. The IETF funds this program in the hope that these scientists will collect sufficient published data to help them qualify for future federal funding that will lead to better treatments and a cure. IETF members receive two copies a year of the member magazine, Tremor Talk and three copies of the research newsletter, The Scoop on Tremor. Articles in both publications are written for the non-medically trained person and discuss recent advances in research, coping techniques and topics of general interest to those with ET. Medical and research articles are written by physicians and researchers who work with patients with ET and/or study ET in laboratories. The International Essential Tremor Foundation is based in Lenexa, Kansas.

Proper citation: International Essential Tremor Foundation (RRID:SCR_001163) Copy   

•   Source: SciCrunch Registry