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Here, we present our latest release deepTools2 and its associated web server, which is based on the well-known Galaxy platform 6. This ensures that users lacking access to specialized resources and servers can still benefit from a simple and flexible framework for reproducible analysis.
The package has been designed to take as input files some of the most established formats in the deep sequencing field, such as BAM for aligned reads, bigWig for scores e. All tools come with a large number of options that can be used to fine-tune analyses or filter input datasets for faster data exploration. The visualizations and output files encompass highly customizable, publication-ready images as well as genome-wide scores in bigWig or bedGraph format and tab-separated summaries, e.
Table 1. Open in a separate window Users can upload data from their computers, e. In addition, we have added more commonly used reference genomes and annotations to the web server's data library. Moreover, comprehensive test data is provided to allow users to easily explore the server's functionality without the need to upload their own data. Nat Commun. Computational proteomics tools for identification and quality control. Epub Jul 1.
LILY-lipidome isotope labeling of yeast: in vivo synthesis of 13 C labeled reference lipids for quantification by mass spectrometry. Epub May 5. PeptideMapper: efficient and versatile amino acid sequence and tag mapping.
A novel physiological role for cardiac myoglobin in lipid metabolism. Epub Feb Mol Cell Proteomics. Epub Jan Methods Mol Biol. Protein lipid modifications--More than just a greasy ballast. Kurze , K. Michie, S. Dixon, A.
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Bando, Y. Katou, M. Komata, H. Tanaka, T. Itoh, T. Sutani, and K. Csm3, Tof1, and Mrc1 form a heterotrimeric mediator complex that associates with DNA replication forks.
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Mori, Y. Matsumoto , T. Shibata, K. Rec8 guides canonical Spo11 distribution along yeast meiotic chromosomes. Tanaka, Y. Yagura, K. Saitoh, T. Itoh, H. Araki, M. Bando , and K. Ctf4 coordinates the progression of helicase and DNA polymerase alpha. Deardorff, D. Kaur, S. Tandy, T. Kondoh, E. Rappaport, N.
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Urano, Y. Sakaki, K. Sasano, S. Takahashi, T. Kitamura, Y. Ouchi, H. Aburatani, and S. Amyloid precursor protein is a primary androgen target gene that promotes prostate cancer growth. Cancer Res. Mishiro, K. Ishihara, S. Hino, S. Tsutsumi, H. Aburatani, K.
Shirahige, Y. Kinoshita, and M. Architectural roles of multiple chromatin insulators at the human apolipoprotein gene cluster. Sutani, T. Kawaguchi, R. Kanno, T. Itoh, and K. Nishizawa, T. Komai, Y. Itoh, and A. Nutrient-regulated antisense and intragenic RNAs modulate a signal transduction pathway in yeast. Nakamura, A. Okamoto, Y. Katou, C. Yadani, T. Shitanda, C. Kaweeteerawat, T.
Masukata, and T. Rad51 suppresses gross chromosomal rearrangement at centromere in Schizosaccharomyces pombe. Sadaie, R. Kawaguchi, Y. Arisaka, K. Tanaka, K.
Shirahige, J. Balance between distinct HP1 family proteins controls heterochromatin assembly in fission yeast. Mol Cell Biol. D'Ambrosio, C.
Schmidt, Y. Katou, G. Kelly, T. Shirahige, and F. Identification of cis-acting sites for condensin loading onto budding yeast chromosomes. Lou, M. Komata, Y. Katou, Z. Guan, C. Reis, M. Budd, K. Cell 32, K. Bando, B. Koch, E. Schirghuber, S.