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.
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.
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.
A computational pipeline that discovers motifs in peak sequences, compares them with databases, exports putative binding sites for visualization in the UCSC genome browser and generates an extensive report suited for both naive and expert users. RSAT peak-motifs relies on time- and memory-efficient algorithms enabling the treatment of several thousand peaks within minutes.
Allows users to store, visualize and analyze epigenomics and transcriptomics data using a biologist-friendly web interface, without the need for programming expertise. Predefined pipelines allow users to download data, visualize results on a genome browser, calculate RPKMs (reads per kilobase per million) and identify peaks. Advanced capabilities include differential gene expression and binding analysis, and creation of average tag -density profiles and heatmaps.
Identifies protein–DNA binding events in small bacterial and archaeal genomes. Pique facilitate downstream data visualization, curation and analysis. It also provides a suitable platform for large-scale studies of the structure and dynamic remodeling of gene-regulatory networks. This method is able to operate on systems that have genomic complexities such as IS elements, gene dosage polymorphisms and accessory genomes.
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.
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.
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.
Allows annotation, bulk summarization, and visualization of genomic intervals over predefined genomic annotations. Genomation is an R package designed for interrogating diverse types of genomic intervals with or without scores. The software reduces the time needed for data processing and biological inference by providing several functions. It can be used with a variety of genomic interval file types.
Provides a visualization tool available as plug-in for the Galaxy platform. CHROMATRA allows detailed yet concise presentations of data derived from ChIP-chip or ChIP-seq experiments by visualizing enrichment scores across genes or other genomic features while accounting for their length and additional characteristics such as gene expression. It integrates into typical analysis workflows and enables rapid graphical assessment and comparison of genome-wide data at a glance.
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.
Aggregation plots are frequently used to evaluate signal distributions at user-interested points in ChIP-Seq data analysis. agplus enables rapid and flexible generation of text tables tailored for aggregation plots from which users can easily design multiple groups based on user-definitions such as regulatory regions or transcription initiation sites.
Creates metagene plots. MetaPlotR generates metagene plots of nucleotide modifications, protein binding sites or any other transcriptomic sites. It works for any organism for which a genome and transcript annotation is available through the UCSC genome browser database. The tool can project the sites occur onto a virtual transcript space and plots the metagene coordinates as a histogram or density plot.
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.
Analyzes local epigenetic neighborhood of a set of single nucleotides polymorphisms (SNPs). SNPhood is a package allowing users to exploit data from next generation sequencing (NGS) by offering a mean to (i) discover allelic bias through regions of interest (ROI); (ii) browse and view genotype-dependent binding patterns and (iii), make genotype-dependent comparisons and grouping of the binding pattern across ROI and samples.
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.
Provides summary statistics in graphs and offering several commonly demanded analyses. ChIPseek integrates HOMER et BEDTools software and enables peak annotation, locations, sequences and statistics such as charts and histograms for the visualization of the properties of the peaks. Users can explore peaks further via an UCSC genome browser. It contains filter tools to select interested peak subsets based on peak lengths and other characterictics.
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.
Generates a positional correlation histogram for two specific genomic features. ChIP-Cor enables users to obtain aggregation plots (APs) for peak lists with a great variety of target features. The software offers several options for scaling the abundance of the target feature. It reads ChIP-Seq tag positions and can create a positional correlation histogram for two genomic features. This tool suits for educational purposes.
Provides visualization and postprocessing options. MotIV is a program that assists users to identify biologically relevant combinations of motifs. It includes functions for visualizing and annotating motifs and identifies motif combinations that have nonrandom spatial relationships. Moreover, this program offers features for plotting the frequency distributions of the distance between motif occurrences and peak centers.
Allows peak calling, visualization, quality check and Polymerase Chain Reaction (PCR) bias filtering of ChIP-seq data. DROMPA calls peaks by comparing the read distribution of the ChIP sample with that of the corresponding input sample. The software identifies peaks as bar graph protein-binding sites when the peaks are sharp (approximately 1 kbp) and when they are broad (approximately 1 Mbp). It can accept multiple mapped reads (reads mapped on multiple loci of the reference genome).
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.
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.
Enables the broad adoption of next generation sequencing (NGS) based inquiries. dictyExpress is a web application designed for exploration of transcriptomics datasets. It allows users to select among experiments and specify genes to analyze; visualize the expression time courses of those genes; identify gene clusters; examine pre-processed differential expression datasets; and perform Gene Ontology (GO)-term enrichment analysis.
Allows peak-calling of replicated ChIP-seq experiments. Sierra platinum provides a variety of quality measures together with integrated visualizations supporting the assessment of the replicates and the resulting peaks, as well as steering the peak-calling process. It outperforms currently available methods using a newly generated benchmark data set and using real data from the NIH Roadmap Epigenomics Project.
Allows clustering, alignment and clustering of epigenomic marks. DGW is based on an algorithm that enables construction of robust speech recognizers undeterred by the variability in pitch and speed of enunciation. The software can align genomic landmarks such as transcription start sites (TSSs) and first splicing sites (FSSs) on real epigenomic data from the ENCODE project. The software can be useful for exploratory data analysis of high throughput epigenomic data sets.
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.
A powerful tool that accurately identifies functional regions of interest (ROIs) on the genome where a genomic signal significantly deviates from the general genome-wide behavior. HATSEQ also includes a number of built-in post-analyses with which biological meaning can be attached to the detected ROIs in terms of gene pathways and de-novo motif analysis, and provides different visualizations and statistical summaries for the detected ROIs. In addition, HATSEQ has an intuitive graphic user interface that lowers the barrier for researchers to analyze their data without the need of scripting languages.
Provides tools for ChIP-Seq spike-in normalization, assessment and analysis. ChIPSeqSpike is an application that includes visual assessment of the data with meta-profiles, heatmaps, boxplots, correlation, and heatscatter plots. It offers a fast way to process the data through different modes and provides publication quality figures through a well-defined set of functions.
Decrypts key biological features from chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) data. ChIPdig aims to assist experimentalists process multi-sample ChIP-seq data. It can map reads to a reference genome, normalize and compare ChIP-seq data sets corresponding to different targets or conditions, display coverage in a set of regions thanks to heatmaps and a comparative metaplot.
Implements a flexible way to plot genome-wide data in many forms. Heatmaps is a software which provides functions for plotting heatmaps of genome-wide data across genomic intervals, such as ChIP-seq signals at peaks or across promoters. This R package also offers to users several functions for investigating sequence features.
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.
Plots the short reads binding profiles of a ChIP-seq experiment. D-peaks is a a ChIP-seq result analysis tool which draws a precise representation of several ChIP-seq experiments along the genomes in a few simple steps. Some options, such as the absolute (and the relative) genomic position, the DNA strand and some other aesthetic possibilities (labels and scale of the axes, colors of the peaks, etc.) must be specified to obtain the resulting figure.
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