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.
A freely available Galaxy-based web server for processing and analysing ribosome profiling data with the visualization functionality provided by GWIPS-viz. RiboGalaxy offers researchers a suite of tools specifically tailored for processing ribo-seq and corresponding mRNA-seq data. Researchers can take advantage of the published workflows which reduce the multi-step alignment process to a minimum of inputs from the user. Users can then explore their own aligned data as custom tracks in GWIPS-viz and compare their ribosome profiles to existing ribo-seq tracks from published studies. In addition, users can assess the quality of their ribo-seq data, determine the strength of the triplet periodicity signal, generate meta-gene ribosome profiles as well as analyse the relative impact of mRNA sequence features on local read density.
Allows users to analyses sequencing data from ribosome profiling experiments. riboSeqR provides a set of methods for parsing ribosomal profiling data from multiple samples, aligning to coding sequences, inferring alternative reading frames, and plotting average and transcript-specific behavior of these data. It was developed to enable non-specialists to parse aligned Ribo-seq data, to identify the predominant lengths of ribosomal fragments and the codon positions to which they map, and to thus identify coding sequences undergoing translation.
A Galaxy toolbox for the analysis of ribosome profiling (Ribo-seq) data. It can be used to detect translational ambiguities, stop codon readthrough events and codon occupancy. It provides a large number of plots for the visualisation of these events.
A dedicated pipeline to identify translation initiation sites (TISs). Ribosome profiling analysis framework features alignment, triplet periodicity analysis, detecting translation initiation sites (TISs), translation of upstream open reading frames (uORFs) and analysis of TIS motifs.
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