kstreet13 / bioc2020trajectories Goto Github PK

Hi,
When I use pca in slingshot function, 1 lineage was predicted, when I use umap, slingshot inferred two lineages.
which one is correct?

Hi bioc2020trajectories official,

When I am following your workshop on the trajectory analysis:

scores <- bioc2020trajectories::imbalance_score(

• rd = reducedDims(sce)$UMAP, 
  

• cl = colData(sce)$pheno$treatment_id,
  

• k = 20, smooth = 40)
  

**Error in loadNamespace(x) :
there is no package called ‘bioc2020trajectories’**

It says, there is no bioc2020trajectories.

I load all the library required according your workshop instruction.

Thank you very much for your help.
Guiling

hi！when I run the following code in vignette：
sce <- bioc2020trajectories::importRawData()
error： Could not connect to database:
unable to open database file。so how to solve the problem?Thanks!!!

Hi @kstreet13,
I am trying to plot a similar figure like your:
is it a umap for your cells colored by your conditions? What kind of dimensionality reduction you use.
do you have the code to produce it?

Hello!

Thanks for the amazing workshop, it was very useful.

I was following the https://hectorrdb.github.io/bioc2021trajectories/articles/TGFB.html for my own single cell analysis, and ran fgsea with the Wald's statistics from the assocRes. However, I realised that if I tried to plot the enrichment plots, the BPs that I expect to be downregulated with increasing pseudotime (in this case cell cycle) are also shown as upregulated in the enrichment plots. Those BPs that I expect to be upregulated (differentiation terms) are correctly shown as upregulated, but if I try to sieve out the downregulated BPs, there is none.

I thought this could be perhaps due to the dfs (6 in my case), thus Wald's test does not look at directionality. I then tried StartvsEnd (df =1) and ran fgsea again, but again the downregulated BPs are flat (no negative enrichment plots).

Can I check if this is because the Wald's test in tradeseq does not look at directionality? This would be a very useful tool for looking at trajectory analysis.

Thanks!

Regards,
Jay

Hi,

I am following the workshop tutorial here:

https://kstreet13.github.io/bioc2020trajectories/articles/workshopTrajectories.html#final-notes-1

I have two conditions. However, I do not know how to plot Figure3 & Figure 4

Trajectory Inference
Differential progression

Would you be kind enough to share the code to plot these figures.

May thanks,

Hi there,

Just doing the rounds tonight. I noticed that you've got an issue installing DelayedMatrixStats during the GitHub Action workflow. Have you got an action plan to tackle that? Perhaps you just need to re-run the workflow again, since the last time it ran seems to be before the latest BioC release.

Let me know if you need any help of advice!
Kevin, (BioC2021 committee)