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.
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.
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, 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).
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.
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 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.