Verified Commit 52c51147 authored by Laurent Modolo's avatar Laurent Modolo
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update gloabal Makefile

parent 81dc3887
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......@@ -145,9 +145,26 @@ traveling salesman problem (TSP)
}
\end{center}
## Slinshot
### Clustering followed by MST and principal curve
\begin{center}
\href{https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4772-0}{
\includegraphics[width=0.8\textwidth]{img/slingshot_1.png}
}
\end{center}
# Cycle detection
## reCAT
\begin{center}
\href{https://www.nature.com/articles/s41467-017-00039-z}{
\includegraphics[width=0.8\textwidth]{img/recat.png}
}
\end{center}
## Evalutation
### Topology
......@@ -223,6 +240,61 @@ Agreement between trajectory differentially expressed features from the known tr
\end{columns}
\end{center}
# Beyond pseudotime
## Waddington OT
\begin{center}
\begin{columns}
\column{0.5\textwidth}
\begin{center}
\href{https://doi.org/10.1016/j.cell.2019.01.006}{
\includegraphics[width=\textwidth]{img/waddington.png}
}
\end{center}
\column{0.5\textwidth}
When we have a scRNASeq time serie we want:
\begin{itemize}
\item to be able to track the evelolution of a given cell
\item identify ancestor cell and descendent
\item identify the changes in the underlaying GRN
\end{itemize}
\vspace{1em}
{\bf We cannot sequence the same cell many time}
\end{columns}
\end{center}
## Waddington OT
\begin{center}
\href{https://doi.org/10.1016/j.cell.2019.01.006}{
\includegraphics[width=\textwidth]{img/OT_1.png}
}
\end{center}
## Waddington OT
\begin{center}
\href{https://doi.org/10.1016/j.cell.2019.01.006}{
\includegraphics[width=\textwidth]{img/OT_2.png}
}
\end{center}
We can find the optime coupling between time $t_i$ and $t_{i+1}$
## Waddington OT
### iPSCs reprogramming
\begin{center}
\href{https://doi.org/10.1016/j.cell.2019.01.006}{
\includegraphics[width=\textwidth]{img/OT_3.png}
}
\end{center}
259,155 cells collected at 39 time points across 18 days
# single-cell RNA-Seq Differential expression analysis *Monday 11 July 2022*
# References
\ No newline at end of file
......@@ -6,19 +6,19 @@ all: 1_scrnaseq_data/scrnaseq_data.pdf \
6_dea/dea.pdf
1_scrnaseq_data/scrnaseq_data.pdf: 1_scrnaseq_data/scrnaseq_data.Rmd
make -C 1_scrnaseq_data/
cd 1_scrnaseq_data/ && make
2_normalization/normalization.pdf: 2_normalization/normalization.Rmd
make -C 2_normalization/
cd 2_normalization/ && make
3_dimension_reduction/dimension_reduction.pdf: 3_dimension_reduction/dimension_reduction.Rmd
make -C 3_dimension_reduction/
cd 3_dimension_reduction/ && make
4_clustering/clustering.pdf: 4_clustering/clustering.Rmd
make -C 4_clustering/
cd 4_clustering/ && make
5_pseudo_time/pseudo_time.pdf: 5_pseudo_time/pseudo_time.Rmd
make -C 5_pseudo_time/
cd 5_pseudo_time/ && make
6_dea/dea.pdf: 6_dea/dea.Rmd
make -C 6_dea/
\ No newline at end of file
cd 6_dea/ && make
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