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MSR
Enables analysis and visualization of the information content of genomic signals. MSR is a method, adapted from an image segmentation algorithm and inspired by multiscale approaches for classifying image texture patterns. The software enables global analysis of genomic data in an unbiased manner with respect to the spatial scales on which biological information is encoded. It was used to analyze measurements of transcription factor binding, covalent histone modifications and DNA methylation, as well as genomic annotations and sequence-derived data.
Trawler
Detects motifs in large scale chromatin-immunoprecipitation (ChIP) data. Trawler is a program that can be run according two different manners: (i) a standalone version providing a pipeline that generates position weight matrices (PWMs) from the extraction and clustering of over-represented motifs; and (ii) a web application supplying the possibility to submit sequences in both FASTA or BED format, to rank predicted motifs by conservation score as well as to produce a set of background sequences.
Epiviz
An interactive visualization tool for functional genomics data. Epiviz supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. Epiviz sets a precedent for genomic data analysis collaborative workflows by enabling reproducible and shareable steps, and allowing custom user code to be dynamically incorporated, while guaranteeing the security and integrity of user data.
VAP / Versatile Aggregate Profiler
Produces profiles of genomic datasets over groups or regions of interest (ROI) by using an absolute or relative method. VAP uses a simple gene list to generate individual or aggregate graphs of the genomic signal via a customizable number of reference points. This software allows up to six reference points to delimit sections of interest to avoid contamination of the signal from adjacent features. The vap_interface module performs the graphical representation whereas the vap_core handles the command line.
ChIPseeker
Annotates ChIP-seq data analysis. ChIPseeker supports annotating ChIP peaks and provides functions to visualize ChIP peaks coverage over chromosomes and profiles of peaks binding to TSS regions. Comparison of ChIP peak profiles and annotation are also supported. Moreover, it supports evaluating significant overlap among ChIP-seq datasets. Currently, ChIPseeker contains 15,000 bed file information from GEO database. These datasets can be downloaded and compare with user's own data to explore significant overlap datasets for inferring co-regulation or transcription factor complex for further investigation.
PAVIS / Peak Annotation and VISualization
Allows to annotate and visualize ChIP-seq peak data. PAVIS is a web-based tool designed and developed for ease of use for biologists or bench scientists. The software offers two primary functions: peak data annotation and peak visualization within relevant genomic context. PAVIS annotation report provides summary statistics such as the number of annotated peaks and relative enrichment level in each genomic feature category. The visualization interface is launched directly from the PAVIS annotation report.
SNPhood
A user-friendly Bioconductor R package to investigate, quantify and visualise the local epigenetic neighbourhood of a set of SNPs in terms of chromatin marks or transcription factor binding sites using data from NGS experiments. SNPhood comprises a set of easy-to-use functions to extract, normalize, quantify, and visualize read counts or enrichment over input in the local neighbourhood of regions of interest (e.g. SNPs) across multiple samples (e.g. individuals). Functionalities in SNPhood are largely complementary to and extend current tools used for ChIP-Seq data analysis. We believe that it will be a helpful tool to generate new biological hypotheses by integrating molecular-phenotype data in an unbiased and position-specific manner.
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.
ChAsE / Chromatin Analysis and Exploration
A cross-platform desktop application developed for interactive visualization, exploration and clustering of epigenomic data such as ChIP-seq experiments. ChAsE is designed and developed in close collaboration with several groups of biologists and bioinformaticians with a focus on usability and interactivity. Data can be analyzed through k-means clustering, specifying presence or absence of signal in epigenetic data, and performing set operations between clusters. Results can be explored in an interactive heat map and profile plot interface and exported for downstream analysis or as high quality figures suitable for publications.
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.
Podbat / POsitioning DataBase and Analysis Tool
Allows to visualize, analyze and store genomic positioning data. Podbat is an integrated computational tool develop for use on epigenomics datasets. The software follows a simple flowchart and implements a flexible genome browser in its core. Genomes can easily be imported and updated as the software connects directly to Ensembl, facilitating the use of the latest available annotations. Podbat was optimized using the yeast genomes of S. cerevisiae and S. pombe.
ColoWeb
A web-based service for evaluating the colocation of genomic features. Users submit genomic regions of interest, for example, a set of locations from a ChIP-seq analysis. ColoWeb compares the submitted regions of interest to the location of other genomic features such as transcription factors and chromatin modifiers. To facilitate comparisons among various genomic features, the output consists of both graphical representations and quantitative measures of the degree of colocalization between user’s genomic regions and selected features. Frequent colocation may indicate a biological relationship.
BiasAway
Allows users to generate composition-matched background sequence sets. BiasAway is a program that provides users six approaches for generating a background useful to overrepresentation analyses: (1) mononucleotide shuffled sequences; (2) dinucleotide shuffled target sequence; (3) genomic sequences matched to the mononucleotide GC content of each target sequence; (4) sliding windows of mononucleotide shuffled sequence, 5) sliding windows of dinucleotide shuffled target sequence, and 6) genomic sequences matched in windows of internal mononucleotide GC content for each target sequence.
SraTailor
A simple GUI software tool for visualizing published ChIP-seq raw data. SraTailor automatically converts an SRA into a BigWig-formatted file. Simplicity of use is one of the most notable features of SraTailor: entering an accession number of an SRA and clicking the mouse are the only steps required to obtain BigWig-formatted files and to graphically visualize the extents of reads at given loci. SraTailor is also able to make peak calls, generate files of other formats, process users' own data, and accept various command-line-like options. Therefore, this software makes ChIP-seq data fully exploitable by a wide range of biologists.
SPARTA
Extracts raw Illumina reads to differentially expressed genes. SPARTA is a bacterial RNA-seq analysis tool performing transcriptional profiling experiments using RNA-seq. It enables microbiologists to simplify their researches and provides supplies the ability to incorporate a hands-on approach to next-generation sequencing (NGS) technologies in the classroom. Moreover, it outputs quality analysis reports, gene feature counts and differential gene expression tables and scatterplots.
fluff
A software package that allows for simple exploration, clustering and visualization of high-throughput sequencing experiments. fluff contains three command-line tools to generate publication-quality figures in an uncomplicated manner using sensible defaults. Genome-wide data can be aggregated, clustered and visualized in a heatmap, according to different clustering methods. This includes a predefined setting to identify dynamic clusters between different conditions or developmental stages. Alternatively, clustered data can be visualized in a bandplot. Finally, fluff includes a tool to generate genomic profiles. As command-line tools, the fluff programs can easily be integrated into standard analysis pipelines.
MicroScope
Obsolete
A ChIP-seq and RNA-seq software suite for visualizing and analyzing genomic data, including features to support differential expression analysis, heatmap production, principal component, gene ontology and dynamic network analysis. MicroScope allows the user to magnify any portion of a heatmap by a simple click-and-drag feature to zoom in, within the R programming environment, without any prerequisite programming skills required of the user. MicroScope is designed with large gene expression heatmaps in mind, where individual gene labels overlap and render the text unreadable.
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