SpiecEasi
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zdk123
Sparse InversE Covariance estimation for Ecological Association and Statistical Inference
Hi, Kurtz I performed "spiec.easi" with "MB" using 6 samples including about 200 species. I know the number of samples is insufficient for network inference. I have already performed this...
Hello, Ive been trying to install this package for a week. I installed a bunch of Fortran files and moved libraries but to no avail. Any help would be appreciated....
Hi, Is it possible to implement spiec.easi using an OTU table (that is in a relative abundance format)? The documentation reads "For a matrix, non-normalized count OTU/data table with samples...
Hi! Has anyone managed to install SpiecEasi in a conda environment? Can you tell specification of your environment? thanks S.-
Hello zdk, I am using SPIEC-EASI for making network. For my work, I want to filter my edges with some threshold value such like absolute value over "0.1". But when...
Hi Zachary, I have noticed that the results generated by the qqdplot_comm() function are not as expected. When I use the function to plot data generated from a zero-inflated negative...
Hello, I am trying to do a cross domain analysis on a relatively big microbial dataset. On one hand I have a bacterial abundance matrix with 7000+ columns (aka species)...
I hope that change the output of SpiecEasi into a correlation matrix similar to the downloaded from MENAP will eventually allow me to calculate robustness with the code in this...
Hi, doctor Zachary Kurtz I am interested in making the files like the "amgut2.filt.phy" used when processing analysis with phyloseq, but i found its not possible for me to reproduce...
Dear Zachary, I hope all is well. I wanted to inquire about your pre-print and the beta/rank penalty parameter tuning for model selection. Specifically in your manuscript, you've written :...
