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Showing :
questions
3
votes
2
replies
2.9k
views
How to convert merged_abundance-table into a biom file?
metaphlan
biom
wgs
metagenome
updated 2.2 years ago by
D
▴ 10 • written 3.8 years ago by
dpc
▴ 240
1
vote
1
reply
1.5k
views
Process to merge biom files
metaphlan
biom
wgs
updated 2.3 years ago by
serene.s
• 0 • written 3.8 years ago by
dpc
▴ 240
0
votes
0
replies
610
views
How to map enriched pathways on whole metacyc pathway map?
MetaCyc
2.6 years ago by
dpc
▴ 240
0
votes
1
reply
517
views
Does genes for different subunits of a protein have different KO IDs?
kegg
updated 2.8 years ago by
andres.firrincieli
3.6k • written 2.8 years ago by
dpc
▴ 240
0
votes
4
replies
1.2k
views
How to convert gene names to EC numbers?
database
updated 2.8 years ago by
lieven.sterck
15k • written 2.8 years ago by
dpc
▴ 240
0
votes
6
replies
1.3k
views
How to convert gene names to GO term?
databse
2.7 years ago by
dpc
▴ 240
0
votes
0
replies
379
views
How to find the genes within MetaCyc pathways?
database
2.8 years ago by
dpc
▴ 240
0
votes
0
replies
408
views
How to make a genomic content table that has species as the rows and functions (pathways or genes) on the column?
metagenomics
2.8 years ago by
dpc
▴ 240
0
votes
1
reply
514
views
How to get all the metabolic pathways present within a bacteria species?
database
updated 2.8 years ago by
GenoMax
142k • written 2.8 years ago by
dpc
▴ 240
5
votes
4
replies
2.3k
views
Difference between Meta'omics and Multi'omics
Omics
updated 2.9 years ago by
krassowski.michal
▴ 180 • written 2.9 years ago by
dpc
▴ 240
2
votes
4
replies
2.4k
views
Which formula of Bray-Curtis beta diversity index should be used for microbiome beta diversity analysis?
diversity
updated 3.1 years ago by
antonioggsousa
3.2k • written 3.1 years ago by
dpc
▴ 240
3
votes
3
replies
2.0k
views
How can I get the Shannon and observed alpha diversity Index value?
R
3.1 years ago by
dpc
▴ 240
0
votes
0
replies
883
views
Should I calculate beta diversity with or without rarefaction?
diversity
R
3.1 years ago by
dpc
▴ 240
0
votes
0
replies
862
views
What is the minimum LDA score I can take for LefSe analysis?
sequencing
3.3 years ago by
dpc
▴ 240
2
votes
3
replies
2.4k
views
What is the "Effect Size" in LefSe?
statistics
LefSe
updated 3.4 years ago by
zorbax
▴ 610 • written 3.5 years ago by
dpc
▴ 240
1
vote
1
reply
673
views
Change a column name according to the file name
bash
updated 3.6 years ago by
Ram
43k • written 3.6 years ago by
dpc
▴ 240
3
votes
4
replies
2.1k
views
problem in generating correlation heatmap with significance level
heatmap
updated 3.6 years ago by
Kevin Blighe
87k • written 3.6 years ago by
dpc
▴ 240
0
votes
1
reply
3.7k
views
How to show significance value (P value) in heatmap cells generated with pheatmap?
R
pheatmap
3.6 years ago by
dpc
▴ 240
0
votes
2
replies
1.3k
views
Cytoscape: how to make some node labels vertical?
cytoscape
updated 3.6 years ago by
scooter
▴ 620 • written 3.7 years ago by
dpc
▴ 240
2
votes
1
reply
1.8k
views
How MetaPhlAn calculates relative abundance
wgs
metaphlan
updated 3.7 years ago by
plicht
▴ 20 • written 3.8 years ago by
dpc
▴ 240
0
votes
0
replies
1.0k
views
Can I run LEfSe only with Wilcoxon ranksum but not with kruskal-wallis test?
Lefse
3.7 years ago by
dpc
▴ 240
1
vote
3
replies
4.1k
views
How to change the size of the nodes in Cytoscape according to their relative abundance in co-occurrence network?
cytoscape
updated 3.7 years ago by
zhangdengwei
▴ 210 • written 3.7 years ago by
dpc
▴ 240
6
votes
14
replies
8.2k
views
How to make a species co-occurrence network in Cytoscape?
microbiome
updated 2.4 years ago by
psm
• 0 • written 3.7 years ago by
dpc
▴ 240
7
votes
10
replies
6.5k
views
How can I remove the outliers from a boxplot and fill the groups?
R
statistics
updated 3.8 years ago by
Alex Reynolds
35k • written 3.8 years ago by
dpc
▴ 240
1
vote
5
replies
1.0k
views
How can I extract out lines that contains 'g__' at their end along with the first two line headers? (i.e. only the genus level OTU from metaphlan out…
bash command
3.8 years ago by
dpc
▴ 240
3
votes
7
replies
1.9k
views
Can I use pseudocounts for differential abundance of OTUs?
deseq
updated 3.8 years ago by
antonioggsousa
3.2k • written 3.8 years ago by
dpc
▴ 240
3
votes
9
replies
2.6k
views
How to extract out specific distances from a distance matrix?
wgs
phyloseq
updated 3.8 years ago by
antonioggsousa
3.2k • written 3.8 years ago by
dpc
▴ 240
2
votes
2
replies
5.4k
views
How to extract to columns from a phyloseq sample_data object?
phyloseq
updated 3.8 years ago by
antonioggsousa
3.2k • written 3.8 years ago by
dpc
▴ 240
24
votes
25
replies
8.1k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
3.8 years ago by
dpc
▴ 240
5
votes
4
replies
1.3k
views
bash script for catenating many paired end files
catenation
updated 3.8 years ago by
Mark
★ 1.5k • written 3.8 years ago by
dpc
▴ 240
5
votes
14
replies
6.1k
views
METAPHLAN: Relative abundance to read count
metaphlan
phyloseq
updated 3.8 years ago by
antonioggsousa
3.2k • written 3.8 years ago by
dpc
▴ 240
3
votes
8
replies
1.3k
views
Extract out lines with 's__' into a new file together with first two lines of the file
command
grep
updated 3.8 years ago by
antonioggsousa
3.2k • written 3.8 years ago by
dpc
▴ 240
0
votes
0
replies
657
views
Can I analyse my metagenome profiled data with "Curated Metagenomic Data pipeline"?
metaphlan
curated metagenomic data
3.8 years ago by
dpc
▴ 240
0
votes
3
replies
2.1k
views
Smart BLAST or only BLAST?
blast
protein sequence alignment
3.8 years ago by
dpc
▴ 240
0
votes
1
reply
624
views
protein blast from amino acid sequences
BLAST
sequence alignment
phylogenetic analysis
updated 3.8 years ago by
Mensur Dlakic
★ 27k • written 3.8 years ago by
dpc
▴ 240
1
vote
5
replies
1.7k
views
ERROR in QIIME
qiime
biom
merge
3.8 years ago by
dpc
▴ 240
3
votes
13
replies
5.5k
views
Import metaphlan output to phyloseq
metaphlan
phyloseq
wgs
metagenome
updated 3.8 years ago by
Ram
43k • written 3.8 years ago by
dpc
▴ 240
1
vote
3
replies
2.0k
views
Density vs gene count plot
metagenomics
gene count
wgs
mgwas
updated 3.8 years ago by
antonioggsousa
3.2k • written 3.8 years ago by
dpc
▴ 240
3
votes
8
replies
1.2k
views
Gene count vs Relative gene abundance
metagenomics
wgs
updated 3.8 years ago by
Friederike
8.9k • written 3.8 years ago by
dpc
▴ 240
0
votes
7
replies
1.0k
views
METAPHLAN: Getting genus level resolution but not family level
next-gen
software error
WGS
metaphlan
3.8 years ago by
dpc
▴ 240
1
vote
4
replies
1.6k
views
Softwares for statistitical analysis of MetaPhlAn output
next-gen
sequencing
metaphlan
updated 3.8 years ago by
antonioggsousa
3.2k • written 3.8 years ago by
dpc
▴ 240
0
votes
5
replies
1.8k
views
fastqc result: whether trim off low quality reads or not
fastqc
multiqc
quality_check
updated 3.8 years ago by
swbarnes2
14k • written 3.8 years ago by
dpc
▴ 240
4
votes
6
replies
2.9k
views
Is MAPQ score related to Phred quality score?
MAPQ
Phred quality score
updated 3.8 years ago by
Jeremy Leipzig
22k • written 3.8 years ago by
dpc
▴ 240
0
votes
4
replies
1.4k
views
Rarefaction of sequences before MetaPhlan analysis
wgs
metaphlan
rarefaction
3.8 years ago by
dpc
▴ 240
0
votes
1
reply
1.8k
views
Relative abundance heatmap interpretation
heatmap
microbiome
updated 3.8 years ago by
antonioggsousa
3.2k • written 3.8 years ago by
dpc
▴ 240
1
vote
2
replies
2.5k
views
stacked barplot color choice
phyloseq
metagenomics
16s
R
updated 3.8 years ago by
antonioggsousa
3.2k • written 3.8 years ago by
dpc
▴ 240
1
vote
4
replies
1.1k
views
Cut off for "dist.seqs" and "cluster" step in MOTHUR for "genus" level analysis
mothur
16s
metagenome
3.9 years ago by
dpc
▴ 240
0
votes
1
reply
825
views
Number of OTUs obtained from mothur analysis
mothur
16s
otu
3.9 years ago by
dpc
▴ 240
0
votes
7
replies
2.1k
views
Heatmap of mothur output with Phyloseq
phyloseq
mothur
16s
metagenome
3.9 years ago by
dpc
▴ 240
0
votes
4
replies
1.2k
views
mothur output visualisation with Phyloseq: unable to order the x-axis
phyloseq
R
16s
mothur
updated 3.9 years ago by
Asaf
10k • written 3.9 years ago by
dpc
▴ 240
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