Daniel Burkhardt

I'm also getting an `Error writing to custom.css` but I don't really understand what that means or how to go about fixing it.

I came across this while doing de-testing across a bunch of clustering arrangements withing clusters. I likely won't be the only one to come across this issue! I'll send a...

Hmm okay, I think I'm seeing the issue here. So my guess is that for cases where you're comparing two samples of scRNA-seq, "nb" is the correct noise model for...

Okay thanks, I'll try this. On vacation for a few days but I'll add to my to-do for next week. To explain the use case: I have 8 clusters found...

Okay I can confirm that the empty genes error is handled in the latest version on master. It looks like the wilcoxon function has been renamed to rank_test, but this...

I am having a similar issue following the instructions from the kb velocity tutorial (https://www.kallistobus.tools/kb_velocity_tutorial.html) ``` kb count -i /data/sai/kallisto_indices/human/index.idx -g /data/sai/kallisto_indices/human/transcripts_to_genes.txt -o /data/lab/dat asets/Krishnaswamy_2017_Embryoid_Body_Timecourse/kallisto/EBT0_1A -c1 /data/sai/kallisto_indices/human/cdna_transcripts_to_capture.txt -c2 /data/sai/kallisto_indices/human/intron_transcripts_to_capture.txt -x...

Hi Rohit! You can run MELD on each pair of samples independently (i.e. t1_ctr vs t1_ko; t2_ctr vs tr_ko), then compare the magnitude of the MELD likelihoods _if they were...

This looks pretty clearly like there's minimal overlap between the T1 vs T2 datasets so I would analyze them separately

Hi @MikhaelManurung , thanks for your interest in MELD! I'm actively working to get v1.0.0 onto pypi which has better support for >2 conditional categories. I would prefer to have...

@MikhaelManurung, I talked with @mattamodio and the datasets used in SAUCIE had significant batch effects between samples that needed to be corrected prior to analysis. I'm hesitant to create a...