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HOMER / Hypergeometric Optimization of Motif EnRichment
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Performs peak finding and downstream data analysis for next-generation sequencing analysis. HOMER affords several tools and methods to make use of ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and other types of functional genomics sequencing data sets. This software offers support to UCSC visualization, peaks annotation, quantification of transcripts and repeats or differential features, enrichment and expression.
CEAS / Cis-regulatory Element Annotation System
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A software tool designed to characterize genome-wide protein-DNA interaction patterns from ChIP-chip and ChIP-Seq data. CEAS provides summary statistics on ChIP enrichment in important genomic regions such as individual chromosomes, promoters, gene bodies or exons, and infers the genes most likely to be regulated by the binding factor under study. CEAS also enables biologists to visualize the average ChIP enrichment signals over specific genomic regions, particularly allowing observation of continuous and broad ChIP enrichment that might be too subtle to detect from ChIP peaks alone.
Octopus-toolkit
Examines epigenomic and transcriptomic next generation sequencing (NGS) data. Octopus-toolkit can be used for antibody- or enzyme-mediated experiments and studies for the quantification of gene expression. It can accelerate the data mining of public epigenomic and transcriptomic NGS data for basic biomedical research. This tool provides a private and a public mode: one to process the user’s own data, and the other to analyze public NGS data by retrieving raw files from the GEO database.
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.
ePIANNO / ePIgenomics ANNOtation tool
Helps users to explore the associations between protein-binding event, disease-associated genomic variants, and information of general populations by annotating the ChIP-seq datasets. ePIANNO is a web server that combines SNP information of populations (1000 Genomes Project) and gene-disease association information of GWAS (NHGRI) with ChIP-seq (hmChIP, ENCODE, and ROADMAP epigenomics) data. ePIANNO has a user-friendly website interface allowing researchers to explore, navigate, and extract data quickly.
AnnotateGenomicRegions
Allows submission of a list of genomic regions and displaying of the corresponding annotations in a web page. AnnotateGenomicRegions annotates sets of genomic regions of interest with overlapping and/or neighboring features that are mapped to the genome. Moreover, genomic regions of interest can be derived from experiments such as ChIP-seq, DNase hypersensitive sites sequencing (DNase-seq), methylation profiling using reduced representation bisulfite sequencing (Methyl RRBS), quantitation of small RNAs by massively parallel sequencing (Small RNA-seq), resequencing, and more.
SUPERmerge
Allows the analysis and annotation of coverage islands within individual read alignment (BAM) files of histone modification ChIPseq datasets harboring broad chromatin domains. SUPERmerge allows flexible regulation of a variety of read pileup parameters, thereby revealing how read islands aggregate into areas of coverage across the genome and what annotation features they map to within individual biological replicates. It can be useful for investigating low sample size ChIP-seq experiments.
annotatr
An R package to easily and quickly summarize, and visualize the association of genomic regions with genomic annotations. The annotatr package reports all intersections of regions and annotations, giving a better understanding of the genomic context of the regions. A variety of visualization functions are implemented in annotatr to easily plot numerical or categorical data associated with the regions across the annotations, providing insight into how characteristics of the regions differ across the annotations. We also demonstrate that annotatr is up to 11x faster than the comparable R package, ChIPpeakAnno. Overall, annotatr facilitates easy and fast genomic annotation of genomic regions, enabling a richer biological interpretation of experiments.
geneXtendeR
Evaluates the variability of peak overlap with cis-regulatory elements and proximal-promoter regions of nearest genes. geneXtendeR allows exploration of gene ontology differences at various extensions as interactive network graphics or word clouds. It can analyze unique genes and their associated ChIP-seq peaks between any two upstream extension levels. This tool permits to personalize a ChIP-seq analysis to the tissue-specific, peak caller-specific, and environment-specific details.
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