Offers a way to manage pipelines. Toil supports arbitrary worker and leader failure, with strong check-pointing that allows resumption. It can be employed to run scientific workflows on a large scale in cloud or high-performance computing (HPC) environments. This tool was used to compute gene- and isoform- level expression values for 19 952 samples from four studies.
Offers a platform for population-level analyses. dDocent is an open-source software dedicated to individually barcoded restriction-site associated DNA sequencing (RADseq) data processing. The application employs data reduction techniques and interact with other programs to propose features such as de novo assembly of RAD loci, single nucleotides polymorphisms (SNPs) and indel calling as well as quality trimming or baseline data filtering.
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.
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).
A cloud computing tool for calculating differential gene expression in large RNA-seq datasets. Myrna uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible.
Provides a workflow for RNA-Seq-based differential gene expression (DGE) analysis. RobiNA gathers multiple packages and software with the aim of furnishing a cross-platform processing in four main steps: (i) quality assessment and filtering; (ii) mapping the reads to a user-provided reference genome or transcriptome; (iii) perform the experimental design and (iv) statistical analysis of DGE.
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.
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.
Establishes a central, redistributable workbench for scientists and programmers working with RNA-related data. The RNA workbench builds a sustainable community around it. This platform is unique in combining available tools, workflows and training material, as well as providing easy access for experimentalists. It serves as a central hub for programmers, which can easily integrate and deploy their existing or novel tools and workflows.
A powerful analysis tool of genome-wide mRNA-seq or ChIP-seq data for detecting differentially expressed genes or identifying changes in epigenetic modifications (histone acetylation/methylation patterns). EpiCenter is also capable of performing genome-wide TFBS peaking detection and generating read coverage depth plot data (e.g., WIG files for UCSC genome browser).
A graphical user interface that helps biologists to handle and analyse large data collected in RNA-seq experiments. The novel version of RNASeqGUI combines graphical interfaces with tools for reproducible research, such as literate statistical programming, human readable report, parallel executions, caching, and interactive and web-explorable tables of results. These features allow the user to analyse big datasets in a fast, efficient, and reproducible way.
Aims to reduce the efforts put into basic data processing for next-generation sequencing (NGS). QuickNGS enables data analysis for major applications of NGS in a batch-like operation mode. This pipeline relies on the organization of available metadata in a MySQL database which is used to control the overall workflow composed of specific software applications for different kinds of analysis.
Assists users in manipulating high-throughput sequencing (HTS) data and formats. Picard is a Java toolkit that provides a set of command line scripts. It comprises Java-based utilities that manipulate SAM files, and a Java API for creating new programs that reads and writes SAM files. Both SAM text format and SAM binary (BAM) format are supported. It also works with next generation sequencing (NGS).
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.
Processes 3’ mRNA sequencing data. expressRNA classifies the sites where cleavage and polyadenylation take place. It is able to identify the differentially regulated poly(A) sites. This tool provides a flexible data integrative research platform. It facilitates highly reproducibility for computational analysis and allows users to visualize and share data and results in a user-friendly way.
Serves for processing RNA-Seq data. easyRNASeq is a program that combines the necessary packages in a single wrapper that ensures the pertinence of the provided data and information. It also assists users to circumnavigate RNA-Seq processing pitfalls. Moreover, it introduces functionalities to handle data produced by recent next-generation sequencing (NGS) protocols.
Assists in analyzing RNA-Seq data. RSEQtools contains a set of modules to perform a large variety of tasks including: (i) the quantification of expression values, (ii) the manipulation of gene annotation sets, (iii) the visualization of the mapped reads, (iv) the generation of signal tracks, (v) the identification of transcriptional active regions and several auxiliary utilities.
Provides an integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different experiment types (including RNA-seq, ChIP-seq and Bis-seq) and analysis variants (e.g. paired-end, stranded, spliced and allele-specific), and is integrated in Bioconductor so that its output can be directly processed for statistical analysis and visualization.
Aims to ease high-throughput sequencing (HTS) data analysis by the using of distributed computation. Eoulsan is a framework able to perform its tasks on distributed computers. The application includes batch analyses, a full automation process managing external file locations and distributed file system. It can be run according three modes: standalone, local cluster or cloud computing on Amazon Elastic MapReduce.
Allows users simultaneously perform mRNA and miRNA expression analysis. wapRNA is a web application that includes major processes for the next-generation mRNA or miRNA data analysis, including preprocessing raw sequenced reads, mapping tags to reference sequences, gene expression annotation, and other downstream functional analysis such as detecting differentially expressed genes, Gene Ontology and KEGG pathway analysis for RNA, novel miRNA predication and miRNA target prediction. Executable packages are available for users to build their pipeline locally.