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http://sourceforge.net/projects/kanalyze/

A Java toolkit designed to convert DNA and RNA sequences into k-mers.

Proper citation: KAnalyze (RRID:SCR_001323) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data.

Proper citation: AffyExpress (RRID:SCR_001321) Copy   

•   Source: SciCrunch Registry

http://www.px.nsls.bnl.gov/

Biomedical technology research center that creates optimal facilities and environments and support for macromolecular structure determination by synchrotron X-ray diffraction at the National Synchrotron Light Source for the benefit of outside and in-house investigators. The PXRR innovates new access modes such as Mail-in crystallography, builds new facilities, currently on the X25 undulator, advances automation, develops remote participation software, collaborates with outside groups, teaches novice users, and supports vising investigators with 7-day, 20-hours staff coverage.

Proper citation: Macromolecular Crystallography Research Resource (RRID:SCR_001442) Copy   

•   Source: SciCrunch Registry

https://medicine.yale.edu/keck/nida/yped/

Open source system for storage, retrieval, and integrated analysis of large amounts of data from high throughput proteomic technologies. YPED currently handles LCMS, MudPIT, ICAT, iTRAQ, SILAC, 2D Gel and DIGE. The repository contains data sets which have been released for public viewing and downloading by the responsible Primary Investigators. It includes proteomic data generated by the Yale NIDA Neuroproteomics Center (http://medicine.yale.edu/keck/nida/index.aspx). Sample descriptions are compatible with the evolving MIAPE standards.

Proper citation: YPED (RRID:SCR_001436) Copy   

•   Source: SciCrunch Registry

http://www.anxietyaustralia.com.au/

Anxiety Treatment Australia provides information about anxiety disorders, the treatment options, psychologists around Australia who treat anxiety disorders, group therapy & workshops, support groups, articles, resources and links to other sites. Sponsors: his website is brought to you by Catherine Madigan, a Melbourne Clinical Psychologist who specializes in the treatment of Anxiety Disorders (ABN 51 109 368 630).

Proper citation: Anxiety Treatment Australia: Anxiety Disorder Help, Information and Psychologist List (RRID:SCR_001434) Copy   

•   Source: SciCrunch Registry

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

Software package to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.

Proper citation: beadarray (RRID:SCR_001314) Copy   

•   Source: SciCrunch Registry

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

Software package that supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate.

Proper citation: arrayMvout (RRID:SCR_001317) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/philips_users/

Communnity project to help support the efforts of investigators using Philips Healthcare systems. This clearingsite helps users find forums, mailinglists, etc. that support this community. If you have suggestions for inclusion, let the project admin know!

Proper citation: Philips Users Community (RRID:SCR_001438) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.7/bioc/html/affyQCReport.html

Software package to create a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object.

Proper citation: affyQCReport (RRID:SCR_001318) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.12/bioc/html/maigesPack.html

Software package that uses functions to handle and analyze cDNA microarray data.

Proper citation: maigesPack (RRID:SCR_001351) Copy   

•   Source: SciCrunch Registry

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

A multivariate quality assessment software for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality.

Proper citation: MDQC (RRID:SCR_001352) Copy   

•   Source: SciCrunch Registry

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

Software library that contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. It is motivated by the common observation of phenomena involving large chromosomal regions in tumor cells. MACAT is the implementation of a statistical approach for identifying significantly differentially expressed chromosome regions.

Proper citation: MACAT (RRID:SCR_001350) Copy   

•   Source: SciCrunch Registry

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

Software package that allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting.

Proper citation: nnNorm (RRID:SCR_001354) Copy   

•   Source: SciCrunch Registry

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

Software that graphically displays correlation in microarray data that is due to insufficient normalization.

Proper citation: maCorrPlot (RRID:SCR_001348) Copy   

•   Source: SciCrunch Registry

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

Software to identify differentially expressed genes. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes.

Proper citation: lapmix (RRID:SCR_001347) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.jku.at/software/farms/farms.html

Software using a model-based technique for summarizing high-density oligonucleotide array data at probe level for Affymetrix GeneChips. It is based on a factor analysis model for which a Bayesian maximum a posteriori method optimizes the model parameters under the assumption of Gaussian measurement noise.

Proper citation: FARMS (RRID:SCR_001344) Copy   

•   Source: SciCrunch Registry

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

Software package that allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes).

Proper citation: OCplus (RRID:SCR_001342) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages//2.11/bioc/html/bridge.html

Software package to test for differentially expressed genes with microarray data. It can be used with both cDNA microarrays or Affymetrix chip. The packge fits a robust Bayesian hierarchical model for testing for differential expression. Outliers are modeled explicitly using a $t$-distribution. The model includes an exchangeable prior for the variances which allow different variances for the genes but still shrink extreme empirical variances. The model can be used for testing for differentially expressed genes among multiple samples, and can distinguish between the different possible patterns of differential expression when there are three or more samples. Parameter estimation is carried out using a novel version of Markov Chain Monte Carlo that is appropriate when the model puts mass on subspaces of the full parameter space.

Proper citation: bridge (RRID:SCR_001343) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.12/bioc/html/CALIB.html

Software package that contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estimated from external control spikes.

Proper citation: CALIB (RRID:SCR_001338) Copy   

•   Source: SciCrunch Registry

http://www.morpholinodatabase.org/

Central database to house data on morpholino screens currently containing over 700 morpholinos including control and multiple morpholinos against the same target. A publicly accessible sequence-based search opens this database for morpholinos against a particular target for the zebrafish community. Morpholino Screens: They set out to identify all cotranslationally translocated genes in the zebrafish genome (Secretome/CTT-ome). Morpholinos were designed against putative secreted/CTT targets and injected into 1-4 cell stage zebrafish embryos. The embryos were observed over a 5 day period for defects in several different systems. The first screen examined 184 gene targets of which 26 demonstrated defects of interest (Pickart et al. 2006). A collaboration with the Verfaillie laboratory examined the knockdown of targets identified in a comparative microarray analysis of hematopoietic stem cells demonstrating how microarray and morpholino technologies can be used in conjunction to enrich for defects in specific developmental processes. Currently, many collaborations are underway to identify genes involved in morphological, kidney, skin, eye, pigment, vascular and hematopoietic development, lipid metabolism and more. The screen types referred to in the search functions are the specific areas of development that were examined during the various screens, which include behavior, general morphology, pigmentation, toxicity, Pax2 expression, and development of the craniofacial structures, eyes, kidneys, pituitary, and skin. Only data pertaining to specific tests performed are presented. Due to the complexity of this international collaboration and time constraints, not all morpholinos were subjected to all screen types. They are currently expanding public access to the database. In the future we will provide: * Mortality curves and dose range for each morpholino * Preliminary data regarding the effectiveness of each morpholino * Expanded annotation for each morpholino * External linkage of our morpholino sequences to ZFIN and Ensembl. To submit morpholino-knockdown results to MODB please contact the administrator for a user name and password.

Proper citation: Morpholino Database (RRID:SCR_001378) Copy   

•   Source: SciCrunch Registry