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http://www.bioconductor.org/packages/2.14/bioc/html/mBPCR.html

Software package that estimates the DNA copy number profile to detect regions with copy number changes.

Proper citation: mBPCR (RRID:SCR_001273) Copy   

•   Source: SciCrunch Registry
  

http://bioconductor.org/packages/devel/bioc/html/massiR.html

Software that predicts the sex of samples in gene expression microarray datasets.

Proper citation: massiR (RRID:SCR_001157) Copy   

•   Source: SciCrunch Registry
  

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

Software package for dimension Reduction for Array CGH Data with Minimal Information Loss.

Proper citation: CGHregions (RRID:SCR_001278) Copy   

•   Source: SciCrunch Registry
  

http://www.centerwatch.com

CenterWatch is an online resource for news, directories, analysis, and proprietary market research for clinical research professionals and patients. For patients, CenterWatch is committed to providing information on clinical trials, specific drugs, as well as other essential health and educational resources. On this website, patients can search clinical trials, receive e-mail notifications about specific clinical trials, review results from completed clinical trials, search drug information, learn about volunteering for a clinical trial, read an overview of the clinical trials process and find other health and educational resources. For researchers, CenterWatch offers a wide range of tools and resources to improve patient and investigator recruitment, remain current with industry trends and business practices, and strengthen organizational procedures. CenterWatch also offers information on grant opportunities, and a variety of educational books and publications. Researchers can provide the public with information about their clinical trials by using the Clinical Trials Listing Serviceprovided through CenterWatch, or look up more specific information on medicines and equipment using Drug and Device Pipeline News. Overall, the mission of CenterWatch is to be the leading source of news, directories, analysis, and proprietary market research for clinical research professionals and patients. It is located in Boston, MA. :NIF thanks the :Parkinson's Disease Foundation : :for their referral of this resource to us.

Proper citation: CenterWatch (RRID:SCR_001158) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/2.14/bioc/html/CGHbase.html

Software package that contains functions and classes that are needed by arrayCGH packages.

Proper citation: CGHbase (RRID:SCR_001279) Copy   

•   Source: SciCrunch Registry
  

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

Software package for quantile smoothing and genomic visualization of array data.

Proper citation: quantsmooth (RRID:SCR_001271) Copy   

•   Source: SciCrunch Registry
  

http://bigwww.epfl.ch/thevenaz/registration/

Software that implements a set of C routines for robust, high-quality registration of two volumes, aligning according to a least-squares criterion which is well-suited to intramodal registration tasks. Programming skills are required to attach the ANSI-C routine to whichever system users have. It is available on Unix, Macintosh, and PC.

Proper citation: Intramodal Registration Software (RRID:SCR_001148) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/2.0/bioc/html/SNPchip.html

Software package that contains classes and methods useful for storing, visualizing and analyzing high density SNP data. Originally developed from the SNPscan web-tool, SNPchip utilizes S4 classes and extends other open source R tools available at Bioconductor, including the R packages Biobase and oligo. This has numerous advantages, including the ability to build statistical models for SNP-level data that operate on instances of the class, and to communicate with other R packages that add additional functionality.

Proper citation: SNPchip (RRID:SCR_001269) Copy   

•   Source: SciCrunch Registry
  

https://dalexander.github.io/admixture/download.html

A software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. It uses a block relaxation approach to alternately update allele frequency and ancestry fraction parameters. Each block update is handled by solving a large number of independent convex optimization problems, which are tackled using a fast sequential quadratic programming algorithm. Convergence of the algorithm is accelerated using a novel quasi-Newton acceleration method., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ADMIXTURE (RRID:SCR_001263) Copy   

•   Source: SciCrunch Registry
  

http://phm.utoronto.ca/~jeffh/neuromouse.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 17, 2023.Toolbook(tm) based, interactive graphical database which provides structural, molecular, and genetic information on the adult murine nervous system; and its relevance to human neurobiology. This resource is primarily designed as a platform for users to interact, each sharing knowledge on their own area of expertise, which is compiled to a master database. This hypertext atlas presently comprises more than 1000 pages and is designed to provide a flexible integrated resource for the description and discussion of all forms mammalian neurologic data. Version 4.0 of the NeuroMouse program extends the program's basic framework to include a number of areas in modern molecular neurobiology. This system provides an integrated resource for the characterization and description of mammalian neurological data. Major divisions include: Neural Atlas, Molecular Atlas, Genetics/Surgical Lesion Atlas. Neuromouse has been integrated into our strain-specific three dimensional MRI and surgical atlases of the murine CNS. Database contents: Neural Atlas: - Rotational representation of the murine brain. - Neural structures: visual and alphabetic point and click index of neural structures, pathways and systems. - Brain atlas:photographic serial sections in the coronal, sagittal, and horizontal planes (average plate distance - 300 um). Physical brain distances are also provided as are meta-index grids to allow rapid movement between different planes and regions. # Catalog of primary and immortalized neural cells indexed to relevant neural structures. Molecular Atlas: - Index of neurotransmitters: Acetylcholine, GABA, Glutamate, Aspartate, Glycine, Dopamine, Norepinephrine, Epinephrine, Serotonin (synthesis, distribution, degradation, molecular modules, receptors, subunits, agonists, antagonists, gene structure, localization, physical properties and transgenics are indicated for each item). - Index of neurotrophins / neurokines: NGF, BDNF, NT-3, NT-4/5, CNTF, LIF, Onostain M, IL-6, GDNF, FGF's, S100b (ligand, receptors, expression pattern, physical properties, homologous factors, transgenics/knockouts, chromosomal location, effects of agent, and effects of factors on agent are indicated for each item). - Index of additional neural agents: Bcl-2, TNF/Fas, TGF-beta, P53/Rb, PDGF, EGF family (ligand, receptor, expression patterns, physical properties, homologous factors, transgenics/ knockouts, chromosomal location, effects of agent, effects of factors on agent are indicated for each item). - Molecular biology: Molecular biology of important neural genes with integrated l links, plus selected neural topics (ex. programmed cell death, inducible gene systems, protein motifs, neural gene elements, and selected signal transduction pathways). Genetics Atlas: - Lesion paradigms: Index of common neuronal structural and chemical lesion paradigms. - Selected procedures: description of common neurosurgical, cell tracing, culturing and laboratory procedures. - Neurologic syndromes: Index of important human neurologic syndromes and appropriate animals models. - Neural mutant database: Index and description of naturally occurring and genetically modified murine neurologic mutations; including pages on double knockout animals. Interactive maps of each murine chromosome and human syntenic maps.

Proper citation: NeuroMouse Database (RRID:SCR_001143) Copy   

•   Source: SciCrunch Registry
  

http://med.stanford.edu/tanglab/software/frappe.html

Software using a f frequentist approach for estimating individual ancestry proportion.

Proper citation: frappe (RRID:SCR_001264) Copy   

•   Source: SciCrunch Registry
  

https://www.phoenixpeptide.com/

Commercial antibody supplier that specializes in peptide-related products for research in obesity, cardiovascular disease, and diabetes.

Proper citation: Phoenix Pharmaceuticals (RRID:SCR_001141) Copy   

•   Source: SciCrunch Registry
  

https://cran.r-universe.dev/IPCAPS

Software implementing a population structure analysis algorithm which assigns individuals to subpopulations and infers the total number of subpopulations present. Additional functions have been included that result in improved population assignment accuracy. # Universal genotype data encoding scheme which allows the population analysis of all types of genetic markers; Single Nucleotide Polymorphism (SNP), Short Tandem Repeat (STR) and RFLP. # New termination criterion called ?EigenDev? which is more robust to population sampling, thus provides the better estimation of number of assigned subpopulations (K) and higher accuracy for the analysis of large complex population datasets.

Proper citation: ipPCA (RRID:SCR_001262) Copy   

•   Source: SciCrunch Registry
  

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

Software package that enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. It performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition, it produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes, the link to the respective Ensembl gene web page is reported.

Proper citation: VegaMC (RRID:SCR_001267) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/2.1/bioc/html/VanillaICE.html

Software package using Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays.

Proper citation: VanillaICE (RRID:SCR_001268) Copy   

•   Source: SciCrunch Registry
  

https://www.petermac.org/research/labs/grant-mcarthur

Cancer research laboratory at the Peter MacCallum Cancer Centre which investigates biomarkers identification, compounds for activity as anti-cancer drugs, and small molecule targeted therapies.

Proper citation: Translational Research Laboratory (RRID:SCR_001023) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/~stijn/reaper/reaper.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. Software program for demultiplexing, trimming and filtering short read sequencing data.

Proper citation: Reaper - Demultiplexing trimming and filtering sequencing data (RRID:SCR_001144) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/mutascope/

Software suite to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations.

Proper citation: Mutascope (RRID:SCR_001265) Copy   

•   Source: SciCrunch Registry
  

http://www.codoncode.com/productsservices/phrap.htm#PHRED

A base calling program for DNA sequence traces.

Proper citation: Phred (RRID:SCR_001017) Copy   

•   Source: SciCrunch Registry
  

http://www.wpic.pitt.edu/wpiccompgen/GemTools/GemTools.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software tools for modeling genetic ancestry based on the single nucleotide polymorphism (SNP) information. This package of functions helps the user account for genetic ancestry of a large number of individuals using spectral graph theory and projections to break a large problem into smaller pieces and calculate genetic ancestry information efficiently, i.e., a divide and conquer (dac) strategy. It is completely written in R and runs on any platform that supports R.

Proper citation: GemTools (RRID:SCR_001259) Copy   

•   Source: SciCrunch Registry