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Alternative splicing identification software tools | RNA sequencing data analysis

Alternative splicing is widely recognized for its roles in regulating genes and creating gene diversity. Consequently the identification and quantification of differentially spliced transcripts is pivotal for transcriptome analysis.

Source text:
(Wang et al., 2015) A survey of computational methods in transcriptome-wide alternative splicing analysis. Biomol Concepts.

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Assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. Cufflinks assembles individual transcripts from RNA-seq reads that have been aligned to the genome. This software is able to infer the splicing structure of each gene because reads from multiple splice variants for a given gene can be found in a sample. Quantification of transcript abundances is also possible by preferring a reference annotation to assembling the reads.
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.
Analyzes parallel RNA sequence data to catalog transcripts and assess differential and alternative expression of known and predicted mRNA isoforms in cells and tissues. ALEXA-Seq comprises several functions: (1) creation of a database of expression and alternative expression sequence ‘features’, (2) mapping of short paired-end sequence reads to these features, (3) identification of features that are expressed above background noise while taking into account locus-by-locus noise, or (4) identification of features that are differentially expressed in samples.
AStalavista / Alternative Splicing TrAscriptional LAndscape VISualization Tool And more
Allows identification, extraction and displaying of complex alternative splicing (AS) events from annotated genes. AStalavista is an alternative splicing transcriptional landscape visualization tool for investigating and comparing types and distributions of the different AS events found in whole genome annotations and user provided gene sets. The software enables identification of arbitrarily complex combinations of hitherto described AS events, either visually or by representation in a univocal notation system. It can be used if the sequencing/annotation process has not been completed.
rMATS / replicate Multivariate Analysis of Transcript Splicing
A statistical model and computer program designed for detection of differential alternative splicing from replicate RNA-Seq data. rMATS uses a hierarchical model to simultaneously account for sampling uncertainty in individual replicates and variability among replicates. In addition to the analysis of unpaired replicates, rMATS also includes a model specifically designed for paired replicates between sample groups. The hypothesis-testing framework of rMATS is flexible and can assess the statistical significance over any user-defined magnitude of splicing change. The old version of rMATS was called MATS.
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).
SEASTAR / Systematic Evaluation of Alternative Transcription Start Sites in RNA
Permits identification of alternative first exons (FEs) and alternative tandem transcription start sites (TSSs) and quantification of their expression levels. SEASTAR utilizes a logistic regression method to identify FEs, including novel exons that are not present in the current transcriptome annotation. Furthermore, this tool can be applied to an RNA-seq dataset derived from the time course of reprogramming mouse embryonic fibroblasts (MEFs) into induced pluripotent stem cells (iPSCs).
NGS-Trex / NGS TRanscriptome profile EXplorer
Allows user to upload raw sequences and obtain an accurate characterization of the transcriptome profile. NGS-Trex can assess differential expression at both gene and transcript level. It compares the expression profile of different samples. All comparisons are performed using a custom database which is mainly populated with several sources obtained from the NCBI. The tool allows user to discard ambiguously assigned reads or to assign those reads to all competing genes in the case of ambiguities.
Characterizes and identifies bona fide alternatively spliced transcripts in any non-model system that lacks a reference genome sequence. IsoSeq_AS_de_novo can be applied to a non-model system with limited genetic resources. It returns a list of read alignments which represents AS event candidates. This platform provides better recovery on large transcripts and detects more Alternative Splicing (AS) events than can be recovered from transcriptome assemblies based on short reads.
MAJIQ / Modeling Alternative Junction Inclusion Quantification
Provides a method to detect, quantify and visualize differential splicing between groups of experiments. Two key features distinguish MAJIQ from other algorithms. First, MAJIQ does not quantify whole gene isoforms. Instead, MAJIQ defines a more general concept of “local splicing variations”, or LSVs. Briefly, LSVs are defined as splits in a gene splice graph where a reference exon is spliced together with other segments downstream (single source LSV) or upstream of it (single target LSV). The second important distinguishing element of MAJIQ is that it allows users to supplement previous transcriptome annotation with reliably-detected de-novo junctions from RNA-Seq experiments.
Performs pathway analysis of alternative splicing in RNA-Seq data. PathwaySplice consists of five mains features : (i) a fitted analysis according the number of exons associated with each gene; (ii) a selection bias visualization; (iii) a use of logistic regression to evaluate the presence of bias; (iv) a determination of the significant genes involved in pathway significance; and (v) the generation of an enrichment map made of significant pathways. It can be used with various datasets including user-defined ones.
TSIS / Time-Series Isoform Switch
Detects and characterizes temporal and complex isoform switches. TSIS recognizes pairs of alternative splicing (AS) transcripts with one or more isoform switches and genes with multiple pairs of transcripts which show isoform switches. It is based on score schemes from current methods and incorporates metrics which capture the characteristics of the isoform switches. This tool provides histograms that show the number of switches happening at each time-point.
EBChangePoint / Empirical Bayes Change-Point model
Allows recognition of alternative 3' splice sites (SS) and 5' SS. EB Chang Point does not rely on annotation information. It provides a systematic framework permitting integration of various information when available. This tool pools information across genes to improve detection efficiency. It offers a way for users to choose to address different levels of questions, namely, whether alternative 3' SS or 5' SS happens, and/or where it happens.
Allows identification of isoforms from RNA-seq data. SparseIso is a Bayesian method that considers the reads falling on both splice junctions and exons. In this software, the transcript abundance is sampled considering all candidate isoforms to find a global view of isoform selection. The preference of selecting isoforms is determined by both the expression state and the correlation of isoform structure modeled in the covariance matrix. SparseIso allows the false transcripts to have reasonable low abundance.
CASH / Comprehensive alternative splicing Hunting
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Aims to self-construct alternative splicing (AS) sites and detect differential AS events between samples of RNA-Seq data. CASH (Comprehensive alternative splicing hunting) consists of two major stages: SpliceCons (Splice site Construction) and SpliceDiff (differential AS detection). This tool constructs comprehensive splice sites including known and novel AS sites in cells, and identifies differentially AS events between cells. It can improve the detection of AS events and work on the study of AS regulation and function in cells.
PreTIS / Prediction of translation initiation sites
Redicts the initiation confidence of all reading–frame independent start sites (AUG and all near-cognate codons) located in the 5’ UTR of human mRNA sequences. PreTIS gives access to various calculated sequence-encoded and experimentally shown important sequence properties for translational initiation. In addition, an initiation confidence value for each start site is calculated using an established regression model that is based on recent experimental data.
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).
Facilitates expression-based isoform-level analysis of large-scale TCGA (The Cancer Genome Atlas) multi-cancer RNA-seq data. ISOexpresso is a web application that provides isoform-level expression profiles for genes of interest and creates visualizations. The software includes two functions: (1) the Isoform Expression View function for which delivers condition or tissue specific isoform expression patterns and (2) the User Data Annotation function which offers annotation results of user provided variants via expression-based prioritization of gene isoforms.
Predicts and quantifies the NAGNAG alternative splicing events using the RNA-Seq data. nagnag fills a gap in the development of the tools for the accurate estimation of NAGNAG splicing events and provides the user-friendly summary reports and visualization of NAGNAG splicing events, along with read mapping support, which can be easily incorporated into an automatic pipeline for exploring the alternative splicing or visualization of the coverage profiles. In addition, the tool is capable of identifying and classifying the differential NAGNAG splicing events taking into account the biological replicates.
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.
TRAPLINE / Transparent Reproducible and Automated PipeLINE
Serves for RNAseq data processing, evaluation and prediction. TRAPLINE guides researchers through the NGS data analysis process in a transparent and automated state-of-the-art pipeline. It can detect protein-protein interactions (PPIs), miRNA targets and alternatively splicing variants or promoter enriched sites. This tool includes different modules for several functions: (1) it scans the list of differentially expressed genes; (2) it includes modules for miRNA target prediction; and (3) a module is implemented to identify verified interactions between proteins of significantly upregulated and downregulated mRNAs.
ISVASE / identifying sequence variants associated with splicing events
Recognizes sequence variants associated with splicing events (SVASE) by using RNA-seq data. ISVASE is able to identify SVASEs for both parts of splicing event (or junction) separately. It applies several stringent rule-depended filters and statistical filters in different steps in order to reduce false positives linked to sequencing errors. The tool can remove false positive splicing events by evaluating junction shift events and junction signals.
Splicing Express
Provides a simple and effective way for the identification, annotation and visualization of Alternative Splicing Events (ASEs). Splicing Express is a software suite that provides expression graphics in an intuitive fashion. It is able to extract meaningful information from deep transcriptome data and performs statistical analysis aiming to give significance values to the fold differences between the splicing variants. The complete automation in Splicing Express makes it a useful tool for deep analysis of ASE in any transcriptome.
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