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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.
ICE / Iterative Correction and Eigenvector decomposition
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A computational pipeline that integrates a strategy to map sequencing reads with a data-driven method for iterative correction of biases, yielding genome-wide maps of relative contact probabilities. Iterative correction leverages the unique pairwise and genome-wide structure of Hi-C data to decompose contact maps into a set of biases and a map of relative contact probabilities between any two genomic loci, achieving equal visibility across all genomic regions.
HiTC
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Facilitates the exploration of high-throughput 3C-based data. HiTC allows users to import and export ‘C’ data, to transform, normalize, annotate and visualize interaction maps. It proposes a powerful and extensible framework for visualizing and exploring high-throughput C data and is able to handle both 5C and Hi-C data and offers new functionalities such as standard import, data transformation and integrative visualization methods. The HiTC package is aimed at biologists interested in investigating their data and at biostatisticians involved in the development of new statistical methods which can be applied to C data.
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.
HiC-bench
Allows a comprehensive and reproducible analysis of Hi-C sequencing data. HiC-bench performs complete Hi-C analysis starting with the alignment of reads (fastq files) and ending with the annotation of specific interactions, their visualization and enrichment analysis. Hi-C pipeline integrates Anchoring Topological Domain (TAD) calling HiC-bench using published methods and your own algorithm and performs calculation of boundary scores using your own methods and existing ones. Every pipeline step is followed by summary statistics (when applicable) and visualization of the results. This allows quality control and facilitates troubleshooting. Furthermore, HiC-bench allows parameter exploration and comparison of different methods in a combinatorial fashion. This feature facilitates the design and execution of complex benchmark studies that may involve combinations of multiple parameter/tool choices in each step.
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