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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).

Octopus-toolkit

New
Examines epigenomic and transcriptomic next generation sequencing (NGS) data. Octopus-toolkit can be used for antibody- or enzyme-mediated experiments and studies for the quantification of gene expression. It can accelerate the data mining of public epigenomic and transcriptomic NGS data for basic biomedical research. This tool provides a private and a public mode: one to process the user’s own data, and the other to analyze public NGS data by retrieving raw files from the GEO database.

oneChannelGUI

Facilitates analysis of microarrays and miRNA/RNA-seq data on laptops. oneChannelGUI can be used for quality control, normalization, filtering, statistical validation and data mining for single channel microarrays. It offers a comprehensive microarray analysis for Affymetrix 3′ (IVT) expression arrays as well as for the new generation of whole transcript arrays: human/mouse/rat exon 1.0 ST and human gene 1.0 ST arrays. oneChannelGUI inherits the core affylmGUI functionalities and permits a wider range of analysis allowing biologists to choose among different criteria and algorithms in order to analyze their data. It is a didactical tool since it could be used to introduce young life scientists to the use and interpretation of microarray data. For this purpose various data sets and exercises are available at the oneChannelGUI web site.

aRNApipe / automated RNA-seq pipeline

Analyzes single-end and stranded or unstranded paired-end RNA-seq data. aRNApipe focuses on high performance computing (HPC) environments and the independent designation of computational resources at each stage allowing optimization of HPC resources. It is highly flexible because its project configuration and management options. This tool can be adapted to changes in the current applications and the addition of new functionalities. It allows users to complete primary RNA-seq analysis.

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.

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.

SAPAS

A pipeline for RNA-seq method to research polyA. SAPAS performs a systematic search and evaluation of protocols for typical steps to investigate to what extent these can indeed facilitate RNA-seq data analysis. 29 open-source interfaces and 6 of the more widely used interfaces were evaluated in detail. SAPAS processes the sequencing result using SAPAS method, including quality control, mapping to genome using bowtie, generating cleverage sites, internal priming, clustering cleverage sites.

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.

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.

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.

ST Pipeline

Permits to process and analyze the raw files generated with the Spatial Transcriptomics (ST) method. ST Pipeline enables demultiplexing of spatially-resolved RNA-seq data and robust quality filtering and identification of unique molecules. It is highly customizable with numerous parameter settings. The tool is more robust, efficient and scales better to arrays with higher density. It filters data, aligns it to a genome, annotates it to a reference, demultiplexes by array coordinates and then aggregates by counts that are not duplicates using the Unique Molecular Identifiers.

TRAPLINE / Transparent Reproducible and Automated PipeLINE

Obsolete
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.

systemPipeR

An extensible environment for both building and running end-to-end analysis workflows with automated report generation for a wide range of next-generation sequencing (NGS) applications. Its unique features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software on local computers and computer clusters. A flexible sample annotation infrastructure efficiently handles complex sample sets and experimental designs. To simplify the analysis of widely used NGS applications, systemPipeR provides pre-configured workflows and reporting templates for RNA-seq, ChIP-seq, VAR-seq and Ribo-seq.

hppRNA

Converts the raw fastq files into gene/isoform expression matrix and differentially expressed genes or isoforms. hppRNA is a one-in-all solution composed of four scenarios such as pre-mapping, core-workflow, post-mapping and sequence variation detection. It also turns the identification of fusion genes, single nucleotide polymorphisms (SNP), long noncoding RNAs and circular RNAs. Finally, this pipeline is specifically designed for performing the systematic analysis on a huge set of samples in one go, ideally for the researchers who intend to deploy the pipeline on their local servers.

PRADA

Processes large numbers of raw RNA-sequencing datasets. PRADA works on paired-end sequencing data and is based on: (1) its mapping to both transcriptomic and genome; or (2) its comprehensive repertoire of output information from the incorporated modules. It enables users to compute multiple analytical metrics. It provides different types of information from raw paired-end RNA-seq data: gene expression levels, quality metrics, detection of unsupervised and supervised fusion transcripts, detection of intragenic fusion variants, homology scores and fusion frame classification.

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.

MetaTrans

Analyzes the structure and functions of active microbial communities using the power of multi-threading computers. MetaTrans is designed to perform two types of RNA-Seq analyses: taxonomic and gene expression. It performs quality-control assessment, rRNA removal, maps reads against functional databases and also handles differential gene expression analysis. Its efficacy was validated by analyzing data from synthetic mock communities, data from a previous study and data generated from twelve human fecal samples.

CIPHER

Automates the processing and analysis of several commonly used Next Generation Sequencing (NGS) datasets including: ChIP-seq, RNA-seq, Global Run On sequencing (GRO-seq), micrococcal nuclease footprint sequencing (MNase-seq), DNase hypersensitivity sequencing (DNase-seq), and transposase-accessible chromatin using sequencing ATAC-seq datasets. CIPHER provides an analysis mode that accomplishes complex bioinformatics tasks such as enhancer prediction. It supplies functions to integrate various NGS datasets together.

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.

MaREA / Metabolic Reaction Enrichment Analysis

New
Assists users in investigating cancer metabolism when data on metabolic measurements are not available. MaREA can be used to: (i) rank the reactions according to the variation in their activity observed between different phenotypes and/or experimental conditions, (ii) enrich the map of human metabolic routes with the variation observed in the Reaction Activity Score (RAS) of each reaction, and (iii) stratify samples according to their metabolic activity.

necklace

Automatically combines transcriptomes from difference sources, such as assembly and annotation, into a compact and unified reference. necklace is applicable to any species with an incomplete reference genome. It aligns and counts reads in preparation for testing for differential gene expression and differential transcript usage analysis. This tool provides the following steps: initial assembly, clustering transcripts into gene groupings, reassembly to build the superTranscriptome and finally alignment and counting of mapped reads in preparation for differential expression testing.

zUMIs

Processes raw reads to count tables for RNA-seq data using Unique Molecular Identifiers (UMIs). zUMIs is a pipeline applicable for most experimental designs of RNA-seq data, such as single-nuclei sequencing techniques. This method allows for down sampling of reads before summarizing UMIs per feature, which is recommended for cases of highly different read numbers per sample. zUMIs is flexible with respect to the length and sequences of the barcodes (BCs) and UMIs, making it compatible with a large number of protocols.

Bio-Docklets

Aims to perform basic analysis and interpretation of datasets with minimal effort. Bio-Docklets is an approach for abstracting the complex data operations of multi-step, bioinformatics pipelines for Next Generation Sequencing (NGS) data analysis. It also run a large number of pipeline instances for concurrent analysis of multiple datasets. It enables easy access to NGS data analysis pipelines for non-bioinformatics experts, on any computing environment whether a laboratory workstation, university computer cluster, or a cloud service provider.

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.

viGEN

Combines existing well-known and novel RNA-seq tools for not only detection and quantification of viral RNA, but also variants in the viral transcripts. ViGEN includes 4 major modules: the first module allows to align and filter out human RNA sequences; the second module maps and count (remaining un-aligned) reads against reference genomes of all known and sequenced human viruses; the third module quantifies read counts at the individual viral genes level thus allowing for downstream differential expression analysis of viral genes between experimental and controls groups, and the fourth module calls variants in these viruses.

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.

NextFlow

Enables pipeline development through the adaptation of existing pipelines written in any scripting language. NextFlow is a workflow management system using Docker technology for the multi-scale handling of containerized computation. The software is designed to address numerical instability, efficient parallel execution, error tolerance, execution provenance and traceability. Users can run any current or previous version of a pipeline for any published and properly deposited analyses.