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piPipes
A coordinated set of pipelines, 'piPipes', to analyze piRNA and transposon-derived RNAs from a variety of high-throughput sequencing libraries, including small RNA, RNA, degradome or 7-methyl guanosine cap analysis of gene expression (CAGE), chromatin immunoprecipitation (ChIP) and genomic DNA-seq. piPipes can also produce figures and tables suitable for publication. By facilitating data analysis, piPipes provides an opportunity to standardize computational methods in the piRNA field.
CAGEfightR / Cap Analysis of Gene Expression in R
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Allows identification of transcription start sites (TSSs) and predicted enhancers. CAGEfightR is an R package that was developed for analyzing RNA-Seq, ChIP-Seq and microarrays available for Cap Analysis of Gene Expression (CAGE) analysis. It offers enhancer prediction, methods for robust tag clustering, annotation and visualization. This method can be used on datasets ranging from small-scale experiments to consortia-level projects.
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