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With the advent of next-generation sequencing (NGS), experimental techniques that capture the biological significance of DNA loci or RNA molecules have emerged as fundamental tools for studying the epigenome and transcriptional regulation on a genome-wide scale. The volume of the generated data and the underlying complexity regarding their analysis highlight the need for robust and easy-to-use computational analytic methods that can streamline the process and provide valuable biological insights. Our solution, aPEAch, is an automated pipeline that facilitates the end-to-end analysis of both DNA- and RNA-sequencing assays, including small RNA sequencing, from assessing the quality of the input sample files to answering meaningful biological questions by exploiting the rich information embedded in biological data. Our method is implemented in Python, based on a modular approach that enables users to choose the path and extent of the analysis and the representations of the results. The pipeline can process samples with single or multiple replicates in batches, allowing the ease of use and reproducibility of the analysis across all samples. aPEAch provides a variety of sample metrics such as quality control reports, fragment size distribution plots, and all intermediate output files, enabling the pipeline to be re-executed with different parameters or algorithms, along with the publication-ready visualization of the results. Furthermore, aPEAch seamlessly incorporates advanced unsupervised learning analyses by automating clustering optimization and visualization, thus providing invaluable insight into the underlying biological mechanisms.

Milagrito, a detector sensitive to very high energy gamma rays, monitored the northern sky from 1997 February through 1998 May. With a large field of view and a high duty cycle, this instrument was well suited to perform a search for TeV gamma-ray bursts (GRBs). We report on a search made for TeV counterparts to GRBs observed by BATSE. BATSE detected 54 GRBs within the field of view of Milagrito during this period. An excess of events coincident in time and space with one of these bursts, GRB 970417a, was observed by Milagrito. The excess has a chance probability of 2.8x10-5 of being a fluctuation of the background. The probability for observing an excess at least this large from any of the 54 bursts is 1.5x10-3. No significant correlations were detected from the other bursts.

The Milagrito water Cerenkov detector near Los Alamos, New Mexico, was operated as a sky monitor at energies of a few TeV between 1997 February and 1998 May, including the period of the strong, long-lasting 1997 flare of Markarian 501. Milagrito served as a test run for the full Milagro detector. An event excess with a significance of 3.7 sigma from Markarian 501 was observed, in agreement with expectations.