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deepTools

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A Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting. Users can upload pre-processed files with continuous data in standard formats and generate heatmaps and summary plots in a straight-forward, yet highly customizable manner.

NOISeq

Identifies differentially expressed genes from count data or previously normalized count data. NOISeq empirically models the noise distribution of count changes by contrasting fold-change differences (M) and absolute expression differences (D) for all the features in samples within the same condition. This reference distribution is then used to assess whether the M-D values computed between two conditions for a given gene are likely to be part of the noise or represent a true differential expression.

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).

DEIVA / Differential Gene Expression Interactive Visual Analysis

Enables locating and identifying single or multiple genes in an immediate, interactive, and intuitive manner. DEIVA offers a unique combination of design decisions that enable inspection and analysis of differential gene expression (DGE) statistical test results with an emphasis on ease of use. DEIVA is available for local use or as a web application to interactively identify and locate genes in a hexbin or scatter plot of DESeq2 or edgeR results.

QuickRNASeq

Advances the automation and visualization of RNA-seq data analyses results. QuickRNASeq is a pipeline that significantly reduces data analysts’ hands-on time, which results in a substantial decrease in the time and effort needed for the primary analyses of RNA-seq data before proceeding to further downstream analysis and interpretation. It provides a dynamic data sharing and interactive visualization environment for end users and enable non-expert end users to interact easily with the RNA-seq data analyses results.

htSeqTools

A package with quality assessment, processing and visualization tools for high-throughput sequencing data, with emphasis in ChIP-seq and RNA-seq studies. htSeqTools includes detection of outliers and biases, inefficient immuno-precipitation and overamplification artifacts, de novo identification of read-rich genomic regions and visualization of the location and coverage of genomic region lists. htSeqTools can be a valuable complement for pipelines and advanced analysis strategies.

expressionplot

A software package consisting of a default back end, which prepares raw sequencing or Affymetrix microarray data, and a web-based front end, which offers a biologically centered interface to browse, visualize, and compare different data sets. ExpressionPlot offers the gene expression community an easy-to-use tool for automated analysis of gene expression and RNA processing data. The back end offers a solution to the problem of detecting significant changes in gene expression and RNA processing, while the web-based interface offers data analysis, visualization and browsing tools that realize the biological potential of this new technology.

DeconRNASeq

A package for deconvolution of heterogeneous tissues based on mRNA-Seq data. DeconRNASeq adopts a globally optimized non-negative decomposition algorithm through quadratic programming for estimating the mixing proportions of distinctive tissue types in next-generation sequencing data. It encapsulates the method in a convenient-to-use format. The independent profile-generating module in DeconRNASeq grants freedom to users, who can combine with other R or Bioconductor packages to perform upstream and downstream analysis of NGS data.

RseqFlow

Allows users to characterize and quantify the set of all RNA molecules produced in cells. RseqFlow contains several modules that include: mapping reads to genome and transcriptome references, performing quality control (QC) of sequencing data, generating files for visualizing signal tracks based on the mapping results, calculating gene expression levels, identifying differentially expressed genes, calling coding single nucleotide polymorphisms (SNPs) and producing MRF and BAM files.

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.

RNA CoMPASS / RNA Comprehensive Multi-Processor Analysis System for Sequencing

Analyzes exogenous and human sequences from RNAseq data. RNA CoMPASS is a parallel computation pipeline that provides a graphic user interface built from several open-source programs such as Novoalign and SAMMate. The application reads both the unmapped reads for pathogen discovery and the mapped reads for host transcriptome analysis. The program supports files generated from single-end, paired-end, and/or directional sequencing strategies.

oposSOM

Bundles a series of sophisticated analysis methods with intuitive visualization options to study high-dimensional data with the special focus on gene-centered expression data. It is designed for a broad user community ranging from bioinformaticians with demands for comprehensive analyses in a sophisticated workflow to application-oriented experimenters with needs in intuitive visualization options for their data. The oposSOM package requires the input of gene-centered expression data solely, e.g. as pre-processed microarray intensity data or RNA-seq read counts in log-scale.

SigFuge

Tests significance of clustering in RNA-seq data. SigFuge allows to identify genomic loci exhibiting differential transcription patterns across many RNA-seq samples. It combines clustering with hypothesis testing to identify genes exhibiting alternative splicing, or differences in isoform expression. SigFuge is presented as a method capable of unsupervised discovery of differential isoform events in RNA-seq. This approach of studying gene expression as per-base expression curves along transcriptome coordinates makes it possible to identify differential events without strictly constraining the analysis to proposed exon or transcript boundaries.

GEPIA / Gene Expression Profiling Interactive Analysis

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Enables to perform a diverse range of gene expression analyses. GEPIA is an interactive web application which analyzes the RNA sequencing expression data of 9,736 tumors and 8,587 normal samples from the TCGA and the GTEx projects. It provides customizable functions such as tumor/normal differential expression analysis, profiling according to cancer types or pathological stages, patient survival analysis, similar gene detection, correlation analysis and dimensionality reduction analysis.

TRAPR / Total RNA-Seq Analysis Package for R

Facilitates the statistical analysis and visualization of RNA-Seq expression data. TRAPR provides various functions for data management, the filtering of low-quality data, normalization, transformation, statistical analysis, data visualization, and result visualization. It allows users to build customized analysis pipelines. The tool can be easily applied to other technologies like Serial Analysis of Gene Expression and microarray thanks to its implementation in R.

GE-mini / Gene Explorer

Provides a method for displaying expression profiles of all available tumor and tissue types, while allowing drilling down to detailed views for specific tissue types. Users can investigate genes of interest anywhere by using a smart phone, inspecting an expression body map and exploring the tumor-normal differential expression for a wide arrange of tissue types. GE-mini fills in the gap between cancer genomics big data and the delivery of integrated information to end users.

visgenex

Allows data preparation, analysis and exploration of transcriptome data with t-SNE (t-statistic Stochastic Neighbor Embedding). Visgenex performs better than commonly used methods, offering insight into underlying patterns of gene expression at both global and local scales and identifying clusters of similarly expressed genes. This method can, therefore, be used in conjunction with conventional clustering methods to provide a means to visualize clusters in the context of the entire data set.

Zika-RNAseq-Pipeline

Provides an open source RNA-seq processing pipeline that can be used to extract knowledge from any study that profiled gene expression using RNA-seq applied to mammalian cells, comparing two conditions. Zika-RNAseq-Pipeline enables the extraction of knowledge from typical RNA-seq studies by generating interactive principal component analysis (PCA) and hierarchical clustering (HC) plots, performing enrichment analyses against over 90 gene set libraries, and obtaining lists of small molecules that are predicted to either mimic or reverse the observed changes in mRNA expression.

TBro / Transcriptome Browser

Aggregates sequences, their annotation, expression levels as well as differential testing results. TBro provides an easy-to-use interface to mine the aggregated data and generate publication-ready visualizations. Additionally, it supports users with an intuitive cart system, that helps collecting and analysing biological meaningful sets of transcripts. TBro is a fully featured yet flexible transcriptome browser that supports approaching complex biological questions and enhances collaboration of numerous researchers.

VisRseq

Provides a visual framework for analysis of sequencing datasets. VisRseq is a computationally rich and accessible framework for integrative and interactive analyses without requiring programming expertise. VisRseq provides R apps, which offer a semi-auto generated and unified graphical user interface (GUI) for computational packages in R and repositories such as Bioconductor. To address the interactivity limitation inherent in R libraries, this framework includes several native apps that provide exploration and brushing operations as well as an integrated genome browser. The apps can be chained together to create more powerful analysis workflows.

Cascade

Allows displaying and explores next generation sequencing (NGS) datasets in a rapid and intuitive way by permitting multiple data attributes to be shown simultaneously. Cascade can analyze RNA-seq data, or whole-exome or genome sequencing (WES/WGS). It employs a variety of tunable parameters to highlight specific attributes of genes/features that are of interest to the researcher. This tool allows researchers and clinicians to make transition from data exploration to hypothesis generation.

MiSTIC / Minimum Spanning Trees Inferred Clustering

Visualizes and compares collections of gene expression profiles, instantly highlighting differences and similarities in gene clustering between cancer types or subtypes. MiSTIC should facilitate identification of new prognostic markers and accelerate improvements in the molecular classification of cancers. Its integrative concept greatly improves the accessibility of complex datasets by end-users and enables the generation of hypotheses on mechanisms driving correlated gene expression. It is adaptable to the analysis of any collection of quantitative profiles.

VOE / Visual Omics Explorer

A cross-platform data visualization portal that is implemented using only HTML and JavaScript code. VOE is a standalone software that can be loaded offline on the web browser from a local copy of the code, or over the internet without any dependency other than distributing the code through a file sharing service. VOE can interactively display genomics, transcriptomics, epigenomics and metagenomics data stored either locally or retrieved from cloud storage services, and runs on both desktop computers and mobile devices.

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.

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.

CummeRbund

A tool for visualizing RNA-seq analysis results. CummeRbund takes the various output files from a cuffdiff run and creates a SQLite database of the results describing appropriate relationships betweeen genes, transcripts, transcription start sites, and CDS regions. Once stored and indexed, data for these features, even across multiple samples or conditions, can be retrieved very efficiently and allows the user to explore subfeatures of individual genes, or genesets as the analysis requires.

ViennaNGS

An integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. ViennaNGS comes with functionality for extracting and converting features from common NGS file formats, computation and evaluation of read mapping statistics, as well as normalization of RNA abundance. Moreover, ViennaNGS provides software components for identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser, as well as wrapper routines for a set of commonly used NGS command line tools.

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.

iCanPlot / Interactive HTML5 Canvas Plotting Library

A compelling platform for visual data exploration based on the latest technologies. iCanPlot is a highly interactive tool to visualize tabular data and identify interesting patterns in an intuitive fashion without the need of any specialized computing skills. A module for geneset overlap analysis has been implemented on the Google App Engine platform: when the user selects a region of interest in the plot, the genes in the region are analyzed on the fly. The visualization and analysis are amalgamated for a seamless experience. Further, users can easily upload their data for analysis—which also makes it simple to share the analysis with collaborators.