each peakset are metadata relating to the experiment from which the peakset was derived. Additionally, files containing mapped sequencing reads (BAM//BED) can be associated with each peakset (one for the ChIP data, and optionally another representing a control dataset). " Rcade : R-based analysis of ChIP-seq And Differential Expression data "Rcade is a tool that analyses ChIP-seq data and couples the results to an existing Differential Expression (DE) analysis. A key application of Rcade is in inferring the direct targets of a transcription factor (TF) -- these targets should exhibit TF binding activity, and their expression levels should change in response to a perturbation of the TF. " DESeq DIME: R-package for Identifying Differential ChIP-seq Based on an Ensemble of Mixture Models. "R package that considers an ensemble of finite mixture models combined with a local false discovery rate (fdr) for analyzing ChIP-seq data comparing two samples. This package can also be used to identify differential in other high throughput data such as microarray and DNA methylation." EdgeR : "edgeR is an R/Bioconductor software package for statistical analysis of replicated count data. Methods are designed for assessing differential expression in comparative RNA-Seq experiments, but are generally applicable to count data from other genome-scale platforms (ChIP-Seq, MeDIP-Seq, Tag-Seq, SAGE-Seq etc" About BiocodersHub BiocodersHub brings bioinformatics and social media together in order to unlock the Science CrowdLearning potential. It is a source code focused framework, the idea is simple, instead of asking for general ideas, you can ask for help by submitting