liuxianghui

Dear Yu: I am surprised to find that some pathway, eg carbon metabolism ko01200, can not be plotted with fold change data. It just give a n empty default pathway....

What is the meaning of geneRatio for dotplot of KEGG GSEA enrichment result

3

Just a simple question, when we use dotplot to look at the enrichment results, x axis is Gene Ratio. for enrichKEGG result, I can understand, there are GeneRatio and BgRatio...

Why my metaeuk search is very slow?

3

Dear Sir, Thanks for developing the tool for prediction of euk proteins from contigs. I downloaded the database for gut microbiome gene catalog amino acid sequences fasta: humanGut_IGC.11M.pep.fa from cngb...

I trimmed the reads using trimmomatic first and tried to run Snippy. However, I am surprised to find out the snippy does not take both paired-end reads and unpaired ones...

Error downloading the chembl22 and Zinc

2

[xianghui@login-c01 keras-molecules]$ python download_dataset.py --dataset chembl22 Bus error (core dumped)#################################################################################################################################### | ETA: 0:00:00 1.44 MB/s Please kindly suggest.

Use Plass for euk metagenomics data

2

I want to extract euk genes/proteins from metagenomics data. I want to build a gene/protein catalog for euk genes. Seems that metaeuk is a reference guided approach ( based on...

Error running mpi job with class

1

Dear sir: I have no problem running a single plass job on my Linux cluster. However, I want to try for mpi plass job. Here are the details for the...

npScarf for a metagenome bin?

3

I assume that npScarf is designed for Single species bacteria. Anyhow, I want to check how it works for my bacteria in metagenomics sample. With Illumina MISEQ data, I did...