Verified Commit 81dc3887 authored by Laurent Modolo's avatar Laurent Modolo
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5_pseudo_time: update

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5_pseudo_time/img/monocle_1.png
5_pseudo_time/img/monocle_1.png
5_pseudo_time/img/monocle_1.png
5_pseudo_time/img/monocle_1.png
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......@@ -41,35 +41,187 @@ classoption: aspectratio=169
- Velocity
6. Differential expression analysis (Monday 11 July 2022 - 15:30)
# Continuous clustering
## Pseudo-time
\begin{center}
\begin{columns}
\column{0.5\textwidth}
one RNA-Seq experiment constitutes a {\bf time series}, with each {\bf cell representing a distinct time point} along a continuum.
\column{0.5\textwidth}
\begin{center}
\href{http://www.nature.com/doifinder/10.1038/nbt.2859}{
\includegraphics[width=\textwidth]{img/pseudo_time.png}
}
\end{center}
\end{columns}
\end{center}
## Pseudo-time
\begin{center}
\begin{columns}
\column{0.5\textwidth}
one RNA-Seq experiment constitutes a {\bf time series}, with each {\bf cell representing a distinct time point} along a continuum.
\column{0.5\textwidth}
\begin{center}
\href{http://www.nature.com/doifinder/10.1038/nbt.2859}{
\includegraphics[with=0.8\textwidth]{img/pseudo_time.png}
\includegraphics[width=0.7\textwidth]{img/gene_cluster.png}
}
\end{center}
\end{columns}
\end{center}
# Path detection
## Topology
\begin{center}
\href{http://www.nature.com/doifinder/10.1038/nbt.2859}{
\includegraphics[width=0.8\textwidth]{img/types_of_topology.png}
}
\end{center}
## Monocle 1
\begin{center}
\href{http://www.nature.com/doifinder/10.1038/nbt.2859}{
\includegraphics[width=0.8\textwidth]{img/monocle_1.png}
}
{\bf MST}: Minimum Spanning Tree
\end{center}
## Monocle 1
\begin{center}
\href{http://www.nature.com/doifinder/10.1038/nbt.2859}{
\includegraphics[with=0.8\textwidth]{img/monocle_1.png}
\includegraphics[width=0.7\textwidth]{img/monocle_2.png}
}
\end{center}
\begin{center}
traveling salesman problem (TSP)
\end{center}
## Monocle 2
### Reversed graph embedding: Dimensionality Reduction via Graph Structure Learning
\begin{center}
\href{http://dx.doi.org/10.1038/nmeth.4402}{
\includegraphics[width=0.7\textwidth]{img/monocle_rge.png}
}
\end{center}
## Monocle 3
\begin{center}
\href{http://cole-trapnell-lab.github.io/monocle-release/monocle3/}{
\includegraphics[width=0.7\textwidth]{img/monocle_3.png}
}
\end{center}
## Diffusion pseudotime (DPT)
\begin{center}
\href{http://dx.doi.org/10.1038/nmeth.3971}{
\includegraphics[width=\textwidth]{img/DPT.png}
}
\end{center}
\begin{itemize}
\item Diffusion map: Euclidean distance between points in the embedded space is equal to the "diffusion distance" between probability distributions centered at those points
\item Branching points are identified as points where anticorrelated distances from branch ends become correlated
\end{itemize}
## Wishbone
### k-NN followed by diffusion map
\begin{center}
\href{http://dx.doi.org/10.1038/nbt.3569}{
\includegraphics[width=0.8\textwidth]{img/wishbone.png}
}
\end{center}
# Cycle detection
# Velocity
## Evalutation
### Topology
\begin{center}
\begin{columns}
\column{0.3\textwidth}
\begin{center}
\href{http://www.nature.com/doifinder/10.1038/nbt.2859}{
\includegraphics[width=\textwidth]{img/criteria_1.png}
}
\end{center}
\column{0.7\textwidth}
Compute the distance between the real and infered topology and weight this distance by the edge lenght
\end{columns}
\end{center}
## Evalutation
### Branch assignment
\begin{center}
\begin{columns}
\column{0.3\textwidth}
\begin{center}
\href{http://www.nature.com/doifinder/10.1038/nbt.2859}{
\includegraphics[width=\textwidth]{img/criteria_2.png}
}
\end{center}
\column{0.7\textwidth}
Harmonic mean between Recovery and Relevance
with:
{\bf Relevance} the similarity of all pairs of branches between
the two trajectories using the Jaccard similarity
{\bf Recovery}: the average maximal similarity of all branches in the reference dataset
\end{columns}
\end{center}
## Evalutation
### Cell positions
\begin{center}
\begin{columns}
\column{0.3\textwidth}
\begin{center}
\href{http://www.nature.com/doifinder/10.1038/nbt.2859}{
\includegraphics[width=\textwidth]{img/criteria_3.png}
}
\end{center}
\column{0.7\textwidth}
Quantifies the similarity in cellular positions between two trajectories, by calculating the correlation between pairwise geodesic distances
\end{columns}
\end{center}
## Evalutation
### Cell positions
\begin{center}
\begin{columns}
\column{0.3\textwidth}
\begin{center}
\href{http://www.nature.com/doifinder/10.1038/nbt.2859}{
\includegraphics[width=\textwidth]{img/criteria_4.png}
}
\end{center}
\column{0.7\textwidth}
Agreement between trajectory differentially expressed features from the known trajectory and the predicted trajectory
\end{columns}
\end{center}
# single-cell RNA-Seq Differential expression analysis *Monday 11 July 2022*
......
......@@ -80,9 +80,17 @@ classoption: aspectratio=169
\end{center}
# Parametric versus non-parametric testing
# Differential expression analysis between groups
## Differential expression analysis between $2$ groups
## Between $n$ groups
# Regression analysis
# Multiple testing
# Post-selection inference
# Multivariate Differential expression analysis
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