Annotated record of the detailed examination of Mn deposits from JAPANYON Expedition stations

The cores described in this report were taken on JAPANYON Expedition in June-September 1961 by Scripps Institution of Oceanography from, the R/V Spencer F. Baird. A total of 85 cores and dredges were recovered and are available at Scripps for sampling and study. The coring sites are all in the eastern tropical central Pacific.

Potential temperature in Espartel Sill (Strait of Gibraltar), from 2004-09-30 to 2016-03-02 at 344 meters depth, link to raw data in MATLAB format

Potential temperature measured with a SBE37 at 35.862ºN, 5.97ºW at 344 meters Depth. Data expand from September the 30th, 2004 to March the 2nd, 2016. Original measurement frequency was 30 minutes, the data presented here is a subsampling that extract the coldest temperature found each 12 hours. The time vector corresponds with the moment in which this minimun temperature is observed.

samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files

MOTIVATION: Data from RNA-seq experiments provide us with many new possibilities to gain insights into biological and disease mechanisms of cellular functioning. However, the reproducibility and robustness of RNA-seq data analysis results is often unclear. This is in part attributed to the two counter acting goals of (a) a cost efficient and (b) an optimal experimental design leading to a compromise, e.g., in the sequencing depth of experiments.

RESULTS: We introduce an R package called samExploreR that allows the subsampling (m out of n bootstraping) of short-reads based on SAM files facilitating the investigation of sequencing depth related questions for the experimental design. Overall, this provides a systematic way for exploring the reproducibility and robustness of general RNA-seq studies. We exemplify the usage of samExploreR by studying the influence of the sequencing depth and the annotation on the identification of differentially expressed genes.

AVAILABILITY: Availability: samExploreR is available as an R package from Bioconductor (after acceptance of the paper, download link: http://www.bio-complexity.com/samExploreR_1.0.0.tar.gz).

Evaluation of faecal sampling methods for the analysis of Giardia sp. in companion animals

Dissertação de Mestrado Integrado em Medicina Veterinária