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Johannes Ostner authored Dec 5, 2023
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<span class="byline"><p style="font-size:23px"><strong><a target="_blank" href="https://github.com/bio-datascience/bio-datascience.github.io/blob/master/msc_proposals/MSCThesis_compositional_software.pdf">Integration and visualization of compositional cell population data</a></strong></p></span>
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High-throughput RNA sequencing technologies, such as 16S rRNA and single-cell
RNA sequencing, allow us to determine the type of every cell or microorganism
in a biological sample. Unfortunately, different technologies use different
processing pipelines and data formats on the gene level, often limiting
implementations of novel analysis methods on the cell level to one pipeline.
Also, visualization of such data must be done carefully due to its
compositional nature. <br>
The goal of this M.Sc. Thesis is to develop a data integration and
visualization package in Python to allow for unified analysis of these
types of data. You can read the full proposal <strong><a href="https://github.com/bio-datascience/bio-datascience.github.io/blob/master/msc_proposals/MSCThesis_compositional_software.pdf" target="_blank">here</a></strong>
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<span class="byline"><p style="font-size:23px"><strong><a target="_blank" href="https://github.com/bio-datascience/bio-datascience.github.io/blob/master/msc_proposals/MScProposal_microbiome_cardiovascular.pdf">Learning graphical models to explore the relationship between human gut microbiota and cardiovascular diseases</a></strong></p></span>
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<span class="byline"><strong><p style="font-size:23px"><a target="_blank" href="https://github.com/bio-datascience/bio-datascience.github.io/blob/master/msc_proposals/MSCThesis_scCODA_extension.pdf">Bayesian modeling of high-throughput sequencing data</a></strong></p></span>
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One of the products of our group is scCODA. scCODA is a Bayesian model
can identify compositional changes of cell types. The scCODA model was
specifically designed for use in very low-dimensional settings,
where some properties of high- throughput sequencing data
like zero-inflation and overdispersion are less pronounced. <br>
The goal of this M.Sc. Thesis is to extend this framework, so that it can be
used with higher-dimensional data.
You can read the full proposal <strong><a href="https://github.com/bio-datascience/bio-datascience.github.io/blob/master/msc_proposals/MSCThesis_scCODA_extension.pdf" target="_blank">here</a></strong>
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<span class="byline"><strong><p style="font-size:23px"><a target="_blank" href="https://github.com/bio-datascience/bio-datascience.github.io/blob/master/msc_proposals/MScProposal_alpha.pdf">Alpha diversity measures for microbiome data</a></strong></p></span>
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