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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.

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).

DiffSplice

Detects and visualizes of differential alternative transcription. DiffSplice is an ab initio method to detect alternative splicing isoforms that are differentially expressed under different conditions using high-throughput RNA-seq reads. This software directly localizes where differential splicing occurs, making it easier to identify exons involved in alternative transcription. It estimates the relative proportion of alternative transcription flows in every ASM and calculates the Jensen–Shannon divergence (JSD) to quantify the difference in transcription between samples.

CIDANE / Comprehensive Isoform Discovery and AbuNdance Estimation

A framework for genome-based transcript reconstruction and quantification. CIDANE is engineered to not only assembly RNA-seq reads ab initio, but to also make use of the growing annotation of known splice sites, transcription start and end sites, or even full-length transcripts, available for most model organisms. To some extent, CIDANE is able to recover splice junctions that are invisible to existing bioinformatics tools.

Rockhopper

A comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data. As input, Rockhopper takes RNA sequencing reads output by high-throughput sequencing technology (FASTQ, QSEQ, FASTA, SAM, or BAM files). Rockhopper supports the following tasks: reference based transcript assembly; de novo transcript assembly; normalizing data from different experiments; quantifying transcript abundance; testing for differential gene expression; characterizing operon structures; visualizing results in a genome browser.

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.

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.

LocExpress

Obsolete
Provides nearly real-time expression estimation for novel transcripts in common tissues and cell types. LocExpress is a web server for efficiently estimating expression of novel transcripts across multiple tissues and cell types in human (20 normal tissues/cells types and 14 cell lines) as well as in mouse (24 normal tissues/cell types and 9 cell lines). As a wrapper to RNA-Seq quantification algorithm, LocExpress efficiently reduces the time cost by making abundance estimation calls increasingly within the minimum spanning bundle region of input transcripts.

RNA-seq portal

Includes three types of workflows for different tasks. RNA-seq portal permits users to perform computing and analysis, including sequence quality control, read-mapping, transcriptome assembly, reconstruction and differential analysis. All these workflows support multiple samples and multiples groups of samples and perform differential analysis between groups in a single workflow job submission. This web portal offers bioinformatics software, workflows, computation and reference data and a platform to study complex RNA-seq data analysis for agricultural animal species.

SLIDE

Allows isoform discovery and abundance estimation. SLIDE is a sparse linear model approachthat uses RNA-Seq data to discover mRNA isoforms given an extant annotation of gene and exon boundaries, and to estimate the abundance of the discovered or other specified mRNA isoforms. The software can be used as a downstream isoform discovery tool of de novo gene and exon assembly algorithms. It can be extended to incorporate mRNA isoform information from EST (21), CAGE (19), and RACE (18) data.

TRUFA / TRanscriptome User-Friendly Analysis

Offers a web-based interface that generates the outputs commonly used in de novo RNA-seq analysis and comparative transcriptomics. TRUFA provides a comprehensive service that allows performing dynamically raw read cleaning, transcript assembly, annotation, and expression quantification. It uses highly parallelized steps to obtain annotations in a relatively short time frame. The software is essentially a wrapper of various widely used RNA-seq analysis tools, allowing the generation of RNA-seq outputs in an efficient, consistent, and user-friendly manner, based on a pipeline approach.

RNA-Rocket

Obsolete
A free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations, and the ability to stream results to the bioinformatics resources VectorBase, EuPathDB, and PATRIC. The site also provides a combination of experimental data and metadata, examples of pre-computed analysis, step-by-step guides, and a user interface designed to enable both novice and experienced users of RNA-Seq data.

Oqtans / Online quantitative transcriptome analysis

Provides a Galaxy interface to RNA-seq analysis tools. Oqtans is the online platform for quantitative RNA-seq data analysis. Its integration into the Galaxy framework ensures transparent and reproducible computational analyses. This application is available in five incarnations: (i) as a cloud machine image, (ii) as a public Galaxy instance, (iii) as a git repository, (iv) the Galaxy Toolshed, and (v) a preconfigured share string to launch Galaxy CloudMan using sharing instance functionality.

QuickNGS

A workflow system for laboratories with the need to analyze data from multiple NGS projects at a time. QuickNGS takes advantage of parallel computing resources, a comprehensive back-end database, and a careful selection of previously published algorithmic approaches to build fully automated data analysis workflows. QuickNGS considerably reduces the barriers that still limit the usability of the powerful NGS technology and finally decreases the time to be spent before proceeding to further downstream analysis and interpretation of the data.

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).

MaLTA

A method for simultaneous transcriptome assembly and quantification from Ion Torrent RNA-Seq data. This approach explores transcriptome structure and incorporates a maximum likelihood model into the assembly and quantification procedure. A new version of the IsoEM algorithm suitable for Ion Torrent RNA-Seq reads is used to accurately estimate transcript expression levels. Experimental results suggest increased transcriptome assembly and quantification accuracy of MaLTA-IsoEM solution compared to existing state-of-the-art approaches.

DRUT / Discovery and Reconstruction of Unannotated Transcripts

Allows transcriptome discovery, reconstruction and quantification in partially annotated genomes. DRUT is an annotation-guided general framework. The software incorporates an enhancement of EM algorithm, VTEM, to detect overexpressed reads and/or exons corresponding to the unannotated transcripts and to estimate annotated transcript frequencies. It was validated using three experiments over human RNA-seq data, two experiments on transcriptome quantification and one experiment on transcriptome discovery and reconstruction.

outrigger

Uses junction reads from RNA seq data, and a graph database to create a de novo alternative splicing annotation with a graph database. Outrigger is a Python package and an RNA-seq analysis software that quantify percent spliced-in (Psi) of the events. It finds novel splicing events, including novel exons and was developed to help user to be confident in alternative exon inclusion calculations. It is recommended to use the Anaconda Python Distribution and creates an environment to install outrigger.

IsoInfer

Infers isoforms from short RNA-Seq reads and information concerning exon-intron boundaries and transcription start site (TSS) - poly-A site (PAS) pairs. IsoInfer can calculate the expression levels of isoforms accurately if all the isoforms are known. It can also infer isoforms from scratch when they are sufficiently expressed, by trying to find a minimum set of isoforms to explain the read data. The method works for single-end data and data with both single-end and paired-end read. The software was tested on mouse genes.

bcbio-nextgen

A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The goal is to provide a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.