5_pseudo_time: update

5_pseudo_time/pseudo_time.Rmd

@@ -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*
 

6_dea/dea.Rmd

@@ -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
\ No newline at end of file