Konstantin Zaitsev

Hi @mooreann, It looks like you are trying to install the package using Mac OS X, which I am personally not familiar with. However, from error messages it looks like...

Hi meichendong, At the moment,this $new() constructor can take matrix and data.frame as an input (as a first argument, instead of character GEO identifier) Basically `lo

@methornton You can just provide the expression matrix to a constructor of the Linseed Class (basically matrix objects) I would suggest using something like TPMs, any normalization that already took...

@pushtiks @keremw sorry for the slow replies on my side Weird proportions come from the fact that in both LinSeed and DSA we kinda try to solve sum-to-one constraint as...

@pushtiks Vickie, the inability to fit sum-to-one constraint is rather technical: before we calculate the proportions we first find "pseudo-proportions" these are vectors changes in which correspond to proportions, however,...

Hi @asmariyaz23 , In the paper https://www.ahajournals.org/doi/pdf/10.1161/CIRCRESAHA.118.312804 (figure 7) I was checking the consistency of pathway enrichment: bulk RNA-seq vs scRNA-seq. But in my case, differential expression was done one...