Curator Dashboard

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

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• SciCrunch
• 12 years ago - by Anonymous

Software package to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models.

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• SciCrunch
• 13 years ago - by Anonymous

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.

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• SciCrunch
• 13 years ago - by Anonymous

R software package providing a Graphical User Interface for analysis of Affymetrix microarray data, using the limma package (Linear Models for MicroArray data). While not as powerful as limma to the expert user, it offers a simple point-and-click interface to many of the commonly-used limma and affy functions. You need to have R 1.9.0 or later, Tcl/Tk 8.3 or later (ActiveTcl for Windows, Tcl/Tk Source for Linux/Unix, or X11 Tcl/Tk for MacOSX) and the limma, affylmGUI, and tkrplot R packages. It has been succesfully tested on Windows 2000, Windows XP, RedHat/Fedora Linux, and on Mac OSX with X11.

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• SciCrunch
• 13 years ago - by Anonymous

Software for fitting probe-level models and tools using these models. Probe-level models (PLM) based quality assessment tools.

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• SciCrunch
• 13 years ago - by Anonymous

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.

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• SciCrunch
• 13 years ago - by Anonymous

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.

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• SciCrunch
• 13 years ago - by Anonymous

Blood biobank for the Partners research program, which investigates the affects of genes, lifestyle and environment on human health.

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• SciCrunch
• 16 years ago - by Anonymous

Software functions for performing print-run and array level quality assessment.

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• SciCrunch
• 13 years ago - by Anonymous

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.

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• SciCrunch
• 13 years ago - by Anonymous

Software package for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. The package generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases.

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• SciCrunch
• 13 years ago - by Anonymous

Light-weight software package for normalization and visualization of microarray data using only basic R data types. Software can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.

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• SciCrunch
• 13 years ago - by Anonymous

Portal for a variety of web-based, educational information sources. Subjects include biotechnology, medical genetics, digestive systems and endocrine systems. Animations require a Java-enabled browser.

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• SciCrunch
• 17 years ago - by Anonymous

Software that provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform.

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• SciCrunch
• 13 years ago - by Anonymous

Software package that identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions. It works also for known conditions, for example for RNA-Seq data with two or multiple conditions. RNA-Seq read count data can be provided both by the S4 class Count Data Set and by read count matrices. Differentially expressed transcripts can be visualized by heatmaps, in which unknown conditions, replicates, and samples groups are also indicated. This software is fast since the core algorithm is written in C. For very large data sets, a parallel version of DEXUS is provided in this package. DEXUS is a statistical model that is selected in a Bayesian framework by an EM algorithm. It does not need replicates to detect differentially expressed transcripts, since the replicates (or conditions) are estimated by the EM method for each transcript. The method provides an informative/non-informative value to extract differentially expressed transcripts at a desired significance level or power.

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• SciCrunch
• 13 years ago - by Anonymous

Software package using the GASSCO method for correcting for slide-dependent gene-specific dye bias.

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• SciCrunch
• 13 years ago - by Anonymous

Software to identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).

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• SciCrunch
• 13 years ago - by Anonymous

Software package for a Graphical User Interface for the limma Microarray package.

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• SciCrunch
• 13 years ago - by Anonymous

Software packqge for importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH (Comparative genomic hybridization) experiments.

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• SciCrunch
• 13 years ago - by Anonymous

Software functions for normalization of two-color microarrays by optimised local regression and for detection of artifacts in microarray data.

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• SciCrunch
• 13 years ago - by Anonymous