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An easy-to-use application for microarray, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, AltAnalyze provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichment and more).
COSIE / Corrected Splicing Indices for Exon Arrays
An R function that for a given set of exon arrays corrects for the observed bias and improves the detection of alternative splicing. COSIE adjusts splicing indices for exons, especially for those that belong to differentially expressed genes. For this adjustment, COSIE uses parameters that are specific for each probeset which were trained from a large number of published exon arrays. The downside of this approach is that such parameters cannot be estimated for all probesets on the microarray.
MEAP / Multiple Exon Array Preprocessing
An R package that is designed to preprocess, analyze and visualize Affymetrix GeneChip exon array data. MEAP contains modules for data pre-processing, differential expression analysis, and visualization. Data pre-processing uses a novel background estimation model (PM-BayesBG) and is followed by collective quantile normalization and multi-dimensional expression summarization based on user defined data type (probeset, exon, spliced variant or gene). Differential analysis enables finding biologically interesting targets. The workflow also includes web-based visualization for alternatively spliced events. MEAP produces reliable expression values at exon, alternatively spliced variant and gene levels, which allows generating novel experimentally testable predictions.
IGEMS / Integrated Gene and Exon Model of Splicing
A robust methodology for detection of alternative exon usage (AEU) events using global transcriptome data, yielding results with limited requirement for visual inspection and a high true positive rate. Our meta-analysis indicates that RNA-seq protocols do not provide sufficient quantification of much of the transcriptome (‘read coverage’), which limits alternative splicing analysis of RNA-seq data to only the highest abundance transcripts.
Searches and analyzes alternative splicing (AS) events using Human Transcriptome Array 2.0 (HTA 2.0). EventPointer uses a linear model that broadens its application from plain case-control studies to complex experimental designs. It retrieves a list of all the detected events indicating: 1) the type of event; (2) its fold change and its statistical significance; and (3) the potential protein domains affected by the AS events and the statistical significance of the possible enrichment.
RASA / Robust Alternative Splicing Analysis
Analyzes alternative splicing (AS) of human transcriptome arrays (HTA) platforms and similar exon-junction arrays to reduce the false positives. RASA calculates the expression index of each gene, then detects alternatively spliced exons by requiring significant signal from the exon regions and additional supporting evidence from the corresponding junctions. It also reports all the junctions which are not detected with reliable signals to allow them to be reviewed and selected for further verification. The software was tested on samples of human liver and muscle.
XRAY / Excel Array Analysis
Allows users to identify significant gene expression level and alternative splicing differences between biological states. XRAY is an add-in for Microsoft Excel that provides an interface for analysis and includes several features such as finding of genes with tissue specific expression and with tissue specific alternative splicing, finding of outlier probes and samples or restriction to splicing that may change protein sequence. Users can customize all graphics and results.
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