Cufflinks
Assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
1 - 50 of 56
results
filter_list
Filters
1 - 50 of 56
results
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.
ALEXA-Seq
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.
Subread
Assists users in mapping reads to a reference genome. Subread consists of a seed-and-vote step, that achieves local alignment simultaneously in multiple parts of the read. This strategy uses a large number of short equi-spaced seeds from each read, called subreads. It allows all the subreads to vote on the optimal location for the read.
AltAnalyze
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).
SpliceGrapher
Predicts splice graphs from RNA-Seq and expressed sequence tag (EST) data in order to enhance existing gene annotations. SpliceGrapher includes modules for recognizing alternative splicing (AS) events and for viewing predicted splice graphs along with the evidence employed to construct them. It can make predictions for genes that have low read coverage. This tool assists users to resolve AS events that are otherwise hard to detect from short-read data.
SplitSeek
Identifies splice junctions. SplitSeek allows de novo prediction of splice junctions in short-read RNA-seq data. The software consists of two programs that are executed sequentially. It can detect novel splice events and be used as a way to extend known gene models. The results can be directly uploaded to the UCSC genome browser and used as input to the BEDTools software suite, which enables user to visualize and analyze the predicted events in a genomic context.
AStalavista
Allows to dynamically identify, extract and display 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 whole genome annotations as well as user provided gene sets. Arbitrarily complex combinations of hitherto described AS events can be distinguished, either visually or by representation in a univocal notation system. AStalavista is applicable even if the sequencing/annotation process has not been completed.
SplicePie
A classification of RNA-Seq reads based on three major stages of splicing: pre-, intermediate- and post-splicing. SplicePie offers a number of approaches and solutions to study splicing in more details. The proposed strategy performs well on different sample preparations (sequencing the whole pool of RNAs or capturing a gene with different relative quantities of pre- and mature mRNA).
SUPPA
Allows to analyze differential splicing. SUPPA measures differential splicing between conditions by exploiting the variability between biological replicates to determine the uncertainty in the proportion spliced-in (PSI) values. The software is also able to analyze multiple conditions by computing the pairwise differential splicing between conditions, and can detect groups of events with similar splicing patterns across conditions using density-based clustering.
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.
SpliceTrap
Quantifies local exon inclusion levels in paired-end RNA-seq data. SpliceTrap is a method to generates alternative splicing profiles for different splicing patterns, such as exon skipping, alternative 5’ or 3’ splice sites, and intron retention. It relies on RNA-seq and can determine the inclusion level of every exon within a single cellular condition, without requiring a background set of reads.
SpliceSeq
A tool for investigating alternative mRNA splicing in next generation mRNA sequence data. SpliceSeq displays intuitive visualizations and prioritized lists of results that highlight splicing events and their biological consequences. SpliceSeq unambiguously aligns reads to gene splice graphs, facilitating accurate analysis of large, complex transcript variants that cannot be adequately represented in other formats.
IsoSeq_AS_de_novo
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.
Sircah
An application written in python that detects and visualizes alternative splicing events using spliced alignments. Sircah takes as input transcript models in the GFF3 format allowing the user the flexibility to choose the sources of evidence for the use in detecting alternative transcription.
PSGInfer
Analyzes RNA-Seq data with probabilistic splice graph (PSG) models of gene alternative processing. PSGInfer is able to: (1) construct PSG models from known transcript annotations, (2) estimate maximum likelihood (ML) or maximum a posteriori (MAP) of PSG parameters given an RNA-Seq data set, and (3) predict genes that are differentially processed (DP) between two samples, given RNA-Seq data for each sample.
SNPlice
A computational approach for identifying cis-acting, splice-modulating variants from RNA-seq datasets. SNPlice mines RNA-seq datasets to find reads that span single nucleotide variant (SNV) loci and nearby splice junctions, assessing the co-occurrence of variants and molecules that remain unspliced at nearby exon-intron boundaries. Hence, SNPlice highlights variants preferentially occurring on intron-containing molecules, possibly resulting from altered splicing.
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.
ChopStitch
Retrieves putative exons and builds splice graphs. ChopStitch employs an assembled transcriptome and whole genome shotgun sequencing (WGSS) data to proceed. Using a Bloom filter, it can recognize exon-exon boundaries in de novo assembled RNA-seq data. This tool is able to identify base substitutions in transcript sequences corresponding to sequencing or assembly errors, haplotype variations, or putative RNA editing events.
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.
SparseIso
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
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.
FaRLine / FasterDB RNAseq Pipeline
New
Maps reads on a reference genome and then analyzes them. FaRLine employs a database containing all annotated human splicing variants to work. This tool can serve for the analysis of the effect of metformin treatment on myotonic dystrophy type I (DM1). It aims to improve splicing-related transcriptomic analyses in physiological and pathological situations.
SpliceDetector
New
Recognizes alternative splicing events in human and model organisms. Splice Detector employs transcript identifiers to proceed. It provides the frequency of active splice sites in pre-mRNA. This tool can be used to discover genomic coordinates of query transcript exons. It creates a graph showing the alternative splicing regions and gives an understanding of splice sites and alternative splicing events.
ASIP / Alternative Splicing in Plants
Serve as a starting point for the community to perform additional experiments, including high-throughput methods such as oligonucleotide microarrays studies, to identify functional alternative splicing (AS) events in plants. ASIP uses the characteristics of AS legumes, on the basis of expressed sequence tag (EST) alignments to different genome sequences.
ExonFinder
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).
RAP / RNA-seq Analysis Pipeline
Allows users to analyze sequencing data in multiple steps. The RAP purpose is to investigate the complex transcriptional landscape of eukaryotic transcriptomes through a computationally optimized RNA-Seq data analysis. Users can perform a complete RNA-Seq analysis without any specific technical competence. It offers a web interface and provides different types of results which consist of several tabular and graphical representations.
findAS
A software tool for the analysis of alternatively spliced junctions. FindAS requires RNA-seq data aligned against a reference genome and gene coordinates. Aligned reads are grouped together and groups of overlapping alignments are defined as transcriptional units (TUs). Only TUs unambiguously associated with a single gene prediction are retained and compared against available exon coordinates, allowing to distinguish between different alternative splicing types.
nagnag
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.
SplicingViewer
Investigates splice junctions and alternative splicing (AS) events from RNA-Seq data. SplicingViewer provides a platform dedicated to the visualization of AS patterns. The software first aligns short reads to reference genome, then detect of candidate splice junctions, and, lastly align unmapped short reads to splice junctions. It also displays genome mapping and junction mapping reads.
dSpliceType
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.
Manananggal
Uses to detect alternative splicing events (ASEs). This application written in Java can, through a web application, scans RNAseq data to identify them, and Manananggal can also be launched as a desktop application. The visual output brings a new kind of representation, different from SashimiPlot or SplicingPlot. The ability to select a subset of isoforms allows an easier interpretation of complex alternative splicing events.
spliceR
Sorts alternative splicing (AS) and discovers coding potential. spliceR simplifies downstream sequence analysis by allowing annotation of genomic coordinates of the differentially spliced elements. It is able to detect coding potential of transcripts, determines untranslated region (UTR) and open reading frame (ORF) lengths and predicts whether transcripts are nonsense mediated decay (NMD)-sensitive based on compatible annotated start codon positions and their downstream ORF.
SplicingTypesAnno
Allows users to extract, annotate and analyze alternative splicing (AS) types for sequence alignment files from RNA-Seq. SplicingTypesAnno can detect the novel splicing directly from the aligned raw reads. This tool assists users in management of large set of data by genome-scale and gene-scale functions. Moreover, for the genome scale annotation users can make use of computer clusters with parallel computing feature to accelerate the multiple sample analysis.
Spanki / Splicing analysis kit
A set of tools to facilitate analysis of alternative splicing from RNA-SEQ data.
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.
SpliceVec
New
Serves for distributed feature representation of splice junctions by embedding it in an n-dimensional feature space. SpliceVec contains two variants named genome based SpliceVec (SpliceVec-g) and splicing-context based SpliceVec (SpliceVec-sp) for feature representation of splice junctions. It allows users to capture the splicing signals residing in vicinity of the splice junctions.
ASprofile
Assists in discovering alternative splicing (AS) events in transcripts predicted from RNA-seq data and in comparing them across multiple conditions. ASprofile is a program that can analyze all pairs of transcripts in the sixteen tissues to determine exons included in one transcript and skipped in the other. To realize these operations, this software is composed of several tools: “extract-as”; “extract-as-fpkm”; and “collect-fpkm”.
ASGAL / Alternative Splicing Graph ALigner
New
Estimates alternative splicing (AS) events from an RNA-Seq sample and a gene annotation. ASGAL allows direct comparison of RNA-Seq reads to a splicing graph. It is composed of two functions: (1) a splice-aware aligner of RNA-Seq reads to a splicing graph, and (2) a predictor of AS events supported by the RNA-Seq mappings. This tool is able to translate the alignments from the splicing graph to the genome.
RachetJunction
New
Detects splice junction reads derived from putative recursive sites. RatchetJunction is an algorithm that aligns 4sU-RNAseq reads to its corresponding genome. Then, it extracts reads with an upstream junction matching an annotated 5' splice site and a downstream end mapping to an AGGT. The method can be combined with RachetPair and RatchetScan to increase the identification of candidates recursives sites.
RachetPair
New
Offers a method for determining recursive-site spanning pairs. RatchetPair allows users to highlight read pairs that map to distant genomic sites. The application deduces the presence of intervening recursive splicing by considering the size distribution of inserts in the sequenced library. The approach can be used to optimize the identification of candidates recursives sites, in conjunction with RachetPair and RatchetScan.
LeafCutter
Detects and quantifies novel and existing alternative splicing (AS) events by focusing on intron excisions. LeafCutter identifies variable intron splicing events from short-read RNA-seq data and finds AS events of high complexity. It obviates the need for transcript annotations and overcomes the challenges in determining relative isoform or exon usage in complex splicing events. This tool can be used to discover differential splicing between sample groups, and to map splicing quantitative trait loci (sQTLs).
SPLICIFY
Identifies differentially expressed splice variants on RNA and protein level. SPLICIFY is able to identify condition-specific aberrant splicing events on protein level by performing comparative splice variant analysis on both RNA and protein level. It permits to answer basic research and translational research questions. The tool allows identification of biologically and clinically relevant isoform-specific biomarkers.
RachetScan
New
Forecasts the locations of recursive sites from sawtooth patterns in read density. RachetScan is an algorithm composed of three main steps: (i) RNAseq data processing to summarize read density in each sub-intronic region; (ii) then, sawtooth patterns detection in introns by exploiting a Markov Chain Monte Carlo- (MCMC-) based inference algorithm and; (iii) lastly, inference of the spotted recursive sites. It can be used to investigate complex intronic read patterns.
ASATP / Alternative Splicing Analysis Tool Package
Provides an assortment of methods dedicated to alternative splicing events analysis. ASATP is available as both a standalone software and a web application. It gathers various functions that can be queried separately for (i) identifying and visualizing alternative splicing events; (ii) verifying open reading frame (ORF) changes, (iii) evaluating regulations of alternative splicing and (iv) producing statistical analysis.
SpliCQ
Analyzes next generation sequencing (NGS) data. SpliCQ is a Java library to detect alternative splicing events and major isoforms. The SpliCQ-score allows for a detailed overview on the (differential) expression of known splice variants present or absent in a set of short reads sequenced in NGS experiments. Furthermore, it helps to propose and score novel, yet unknown splice variants.
0 - 0 of 0
results
