Brian Lohman comments

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                                            Brian Lohman

error in alleyoop merge

Hi Tobias, I tried running ```alleyoop merge``` before running ```alleyoop collapse``` but I got the following error: ``` alleyoop merge -o counts.csv /tomato/dev/job/lohman/A6097/single_end/count/17503X*_R1_R2.fastq_slamdunk_mapped_filtered_tcount.tsv Running alleyoop merge for 8 files alleyoop...

Generalize plotting functions to allow use on external results

Hello, I second the request for these plotting tools to be able to use input from fgsea. Thanks, Brian

BEAM() warning: the condition has length >1 and only the first element will be used

Hi @JayalalKJ , Nope, still no idea what's going on. It seems like the Trapnell lab is no longer supporting Monocle 2. I would recommend switching to TradeSeq (https://statomics.github.io/tradeSeq/articles/tradeSeq.html) for...

Question: how to tell "plot_genes_branched_heatmap" the right pre-branch and branch cells?

Similarly, how do you tell which "cell fate" corresponds to which cell state in the resulting heatmap? The default labels are "Cell Fate 1" and "Cell Fate 2". For example,...

pre.py: Segfault while running `preprocess`

Hello, Any updates on this issue? I am experiencing what is likely the same issue as well. I did not track down the source as thoroughly as OP but error...