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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.
SuperTranscript
Visualizes transcript structure for model and non model organisms. SuperTranscript acts as a reference for transcriptome data, where each gene is represented by a single sequence that contains the union of all the exons in their transcriptional order, built from any combination of transcripts, including reference assemblies, de novo assemblies and long-read sequencing. SuperTranscript constructs comprehensive transcriptome sequences in an automated way from any source and can reveal unique insights into the complexities of transcriptomes and identify novel expressed sequence.
Cbrowse
Permits visualization and analysis of transcriptome assemblies and their individual contigs. Cbrowse can decouple interactions with users from interactions with the server. It detects simple sequence repeats for contigs, makes inferences from read alignments about putative polymorphisms and sequencing errors and stores resultant data in a hard-drive file system (HDFS). This tool simplifies close examination of assembly quality, genetic polymorphisms, sequence repeats and/or sequencing errors in transcriptome sequencing projects.
Heat*seq
A web-tool that allows genome scale comparison of high throughput experiments (ChIP-seq, RNA-seq and CAGE) provided by a user, to the data in the public domain. Heat*seq allows users to contextualise their sequencing data with respect to vast amounts of public data in a few minutes without requiring any programming skills. Heat*seq currently contains over 12,000 experiments across diverse tissues and cell types in human, mouse and drosophila. Heat*seq displays interactive correlation heatmaps, with an ability to dynamically subset datasets to contextualise user experiments. High quality figures and tables are produced and can be downloaded in multiple formats.
expVIP / expression Visualization and Integration Platform
Creates a gene expression interface for any species with a transcriptome assembly available. expVIP is an adaptable platform to provide a user-friendly virtual machine implementation that allows breeders and biologists to access this resource on a desktop personal computer. This platform allows comparisons across studies, and the output is viewable as a Web browser interface with intuitive and interactive filtering, sorting, and export options.
GRACOMICS
Enables easy comparison of several methods for analyzing specific omics data platforms by any user. The four omics data employed are active areas of study in bioinformatics. GRACOMICS is composed of 3 modules: Pairwise Correlation Plot to compare two results, Pairwise Interactive Plot to summarize the differences between two results more precisely with a click of a mouse, and Multiple Result Heat Map to compare two or more results comprehensively. Each module is expressed differently, yet can be used to provide mutual supplementation for each other.
RNAbrowse
A user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data. RNAbrowse permits sequencing facilities and, even small, bioinformatic teams to give a user-friendly access to RNA-Seq de novo results, helping biologists to analyse and extract meaningful information from their data. RNAbrowse includes two components: a web-based user interface and an administration command line tool presented here-after.
GOexpress
An R/Bioconductor package for identification and visualisation of gene expression profiles that best classify sample groups according to any known experimental factor. In contrast to most GO term summarisation approaches, GOexpress integrates prior biological knowledge and gene expression data from individual sample replicates to rank molecular pathways based on the capacity of functionally related groups of genes to classify multiple sample groups. Notably, the use of multiple genes for GO-based classification improves the robustness and biological relevance of the resulting interpretations and predictions.
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.
EcoBrowser
Obsolete
Allows searching genome annotations through transcriptome expression profiles of E. coli. EcoBrowser permits users to select genomic regions of interest and then select the transcriptome data to be displayed simultaneously on the search page. It can compare genome-wide expression patterns from independent experiments and genome annotation can be performed by direct comparison. It also assists to discover new transcripts, non-coding RNAs and to generate a detailed description of the transcription unit architecture.
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