Khemlal Nirmalkar

KEGG enrichment analysis for gut microbiome

5

Hello Prof. Yu, I find your clusterProfiler (http://yulab-smu.top/clusterProfiler-book/) a useful tool and tried to follow the tutorial. Since I am working on the gut microbiome and have KEGG pathways for...

Hi, I am a newbie to assembly-annotation work and recently i needed to run prokka twice for the same sets of samples but found a different head for gff files...

Query regarding correlation analysis with heatmap using Microbiome Package

1

Dear Leo Lahti, I am newbie to bioinformatic analysis and trying to make Correlation analysis with heatmap using "Microbiome" and other associated packages by following https://microbiome.github.io/microbiome/Heatmap.html#cont this link. I tried...

labeling sample IDs in emperor beta diversity

1

Hi, Is there any recent update/possibilities on labeling the sample IDs in the beta diversity plot in qiime2? Thanks,

Implementing differential abundance analysis

2

Hi @sbslee I am curious to know, are differential analyses tools like lefse, ANCOM, ALDX2, and/or DeSeq2 for microbiota data out of scope for Dokdo? it would be wonderful to...