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MISO / Mixture of Isoforms
Offers a model for alternative splicing (AS) at exon or isoform level. MISO is a program that uses information in single-end or paired-end RNA-seq data and a Bayesian inference to estimate the probability for a read to be issued from a particular isoform. The program is available through two packages: in C language (fastmiso) or in Python language (misopy). The application supplies confidence intervals (CIs) for: (i) estimating of exon and isoform abundance, (ii) identifying differential expression. It can be applied for analyzing isoform regulation.
Tests for differential usage of exons and hence of isoforms in RNA-seq samples. DEXSeq uses generalized linear models and offers reliable control of false discoveries by taking biological variation into account. It also detects with high sensitivity genes, and in many cases exons, that are subject to differential exon usage. DEXSeq achieves reliable control of false discovery rates by estimating variability for each exon or counting bin and good power by sharing dispersion estimation across features.
Identifies correctly intron retention (IR) events and measured the ratio of retained introns to correctly spliced introns with great accuracy. IRFinder was developed to accurately detect IR from mRNA sequencing data. It implements an end-to-end analysis of retained introns from mRNA sequencing data in multiple species. It also includes alignment via the STAR algorithm, quality controls on the sample analyzed, IR detection, and quantification and statistics for comparing IR levels between multiple samples. IRFinder is a part of bioinformatics tools developed by CNRS to study the impact of intron retention on gene regulation.
A pipeline for the identification of novel exons/alternatively spliced variants (ASVs). ExonFinder is a large-scale comparative analysis of the expressed sequence tag (EST) library from nine grass plants against three crop genomes (rice, maize, and sorghum) and identified 2,879 previously-unannotated exons in the three crops. The library also includes barley (Hordeum vulgare), meadow ryegrass (Festuca pratensis), purple false brome (Brachypodium distachyon), sugarcane (Saccharum officinarum), switchgrass (Panicum virgatum), and wheat (Triticum aestivum).
A generalized framework to systematically investigate the synergistic and antagonistic effects of differential splicing and differential expression. dSpliceType detects and prioritizes a list of genes that are differentially expressed and/or spliced. In particular, the multivariate dSpliceType is among the fist to utilize sequential dependency of normalized base-wise read coverage signals and capture biological variability among replicates using a multivariate statistical model.
IRcall / Intron Retention call
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A computational tool for intron retention (IR) event detection from RNA-Seq data. IRcall calculates the IRscore, which combines information on three aspects: (a) ratio of RPKM within an intron to flanking exons; (b) ratio of read counts within an intron to read counts supporting splice junctions; (c) read coverage within an intron. The introns are ranked by IRscores in descending order, with top-n% introns returned as IR events. Note that top-n% is the user-specified threshold (default top-100%).
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