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Converts the raw fastq files into gene/isoform expression matrix and differentially expressed genes or isoforms. hppRNA is a one-in-all solution composed of four scenarios such as pre-mapping, core-workflow, post-mapping and sequence variation detection. It also turns the identification of fusion genes, single nucleotide polymorphisms (SNP), long noncoding RNAs and circular RNAs. Finally, this pipeline is specifically designed for performing the systematic analysis on a huge set of samples in one go, ideally for the researchers who intend to deploy the pipeline on their local servers.
Enables optimal processing of datasets from different enrichment patterns. Epimetheus is a quantile-based multi-profile normalization tool. Users have the possibility to exclude specific genomic regions like, for example, repetitive elements or any other genomic locations for which artefactual enrichments might be expected. The Epimetheus pipeline involves four main steps: (i) processing of the raw alignment data, (ii) generation of read count intensity (RCI) matrices, (iii) computation of two subsequent levels of normalization (quantile and Zscore) and (iv) generation of outputs and plots.
normR / normR obeys regime mixture rules
A tool for normalization and difference calling in ChIP-seq data. normR performs normalization and difference calling simultaneously to identify genomic regions enriched by the ChIP-procedure. In addition, normR enables the comparison between ChIP-seq data obtained from different conditions allowing for unraveling genomic regions that change their association with the ChIP-target. Lastly, normR is capable to differentiate multiple regimes of enrichment, i.e. broad domains and sharp peaks.
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