Showing : Phyloseq • reset
0
votes
0
replies
70
views
Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER taxonomyassignment phyloseq dada2 Pr2V5
22 days ago Maggie • 0
0
votes
3
replies
1.3k
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 6 months ago by • 0 • written 20 months ago by • 0
2
votes
1
reply
1.8k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 16 months ago by ★ 4.6k • written 16 months ago by ▴ 10
0
votes
0
replies
647
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics metagenomeSeq microbiome phyloseq microbiomeDataSets
17 months ago Mohamed ▴ 30
0
votes
6
replies
1.7k
views
convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 21 months ago by • 0 • written 3.4 years ago by • 0
2
votes
1
reply
4.2k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq Phylogenetics
updated 22 months ago by ▴ 20 • written 22 months ago by • 0
0
votes
3
replies
2.3k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 2.5 years ago by 700 • written 2.5 years ago by • 0
0
votes
1
reply
888
views
error installing phyloseq
phyloseq
updated 2.6 years ago by 4.1k • written 2.6 years ago by • 0
0
votes
3
replies
1.2k
views
Controversial DESEQ2 results
phyloseq DESeq2
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
0
votes
0
replies
663
views
Association between ohylum and genus on microbiome data sets.
phyloseq
2.7 years ago Edmond • 0
0
votes
0
replies
1.8k
views
How to pool phyloseq data?
phyloseq r
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
4
replies
2.5k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 2.9 years ago by 67k • written 2.9 years ago by • 0
0
votes
1
reply
1.0k
views
Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
votes
4
replies
2.2k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
3.0 years ago ymtan • 0
0
votes
1
reply
906
views
Error in 'differential_abundance'
phyloseq devtools
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
votes
0
replies
1000
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq dada2
3.5 years ago Manijeh • 0
0
votes
3
replies
1.3k
views
DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 3.5 years ago by ★ 4.0k • written 3.5 years ago by • 0
0
votes
5
replies
7.5k
views
Problems with installation of 'phyloseq
phyloseq
updated 3.5 years ago by ★ 4.0k • written 3.5 years ago by • 0
0
votes
1
reply
874
views
Purpose of seqtabNoC
phyloseq
updated 3.6 years ago by ★ 4.0k • written 3.6 years ago by • 0
0
votes
0
replies
906
views
Construct Phylogenetic Tree
phyloseq
3.6 years ago klltnq • 0
0
votes
0
replies
750
views
Code Issue
phyloseq
3.6 years ago klltnq • 0
0
votes
3
replies
1.0k
views
Installing Packages repeatedly
phyloseq
updated 3.6 years ago by ★ 4.0k • written 3.6 years ago by • 0
0
votes
1
reply
2.7k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 3.6 years ago by ★ 1.1k • written 3.6 years ago by • 0
1
vote
1
reply
4.5k
views
Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 3.9 years ago by 67k • written 3.9 years ago by • 0
1
vote
3
replies
1.4k
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
4
votes
3
replies
1.4k
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2 phyloseq
updated 4.0 years ago by 43k • written 4.0 years ago by ▴ 10
0
votes
0
replies
1.4k
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
4.1 years ago Chantel • 0
1
vote
2
replies
2.8k
views
Bioconductor install error
phyloseq Bioconductor
4.2 years ago Tess • 0
2
votes
2
replies
2.1k
views
Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
4.3 years ago garfield320 ▴ 30
0
votes
1
reply
1.4k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
0
votes
2
replies
2.3k
views
Error in taxa_are_rows(x) : trying to get slot "taxa_are_rows" from an object (class "otu_table") that is not an S4 object
deseq2 phyloseq
4.6 years ago jaiber.solano.i • 0
0
votes
3
replies
1.3k
views
Nested design- phyloseq_to_deseq
deseq2 Phyloseq Nested
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
0
votes
2
replies
3.3k
views
Problems with bioconductor after updating R to 3.6.2
R 3.6.2 update problems with igraph and phangorn update Phyloseq igraph phangorn Tutorial
updated 5.1 years ago by 25k • written 5.1 years ago by • 0
0
votes
0
replies
1.0k
views
Problems with creating phyloseq bar plots from a table with species data
phyloseq microbiome analysis
6.0 years ago lm795 ▴ 10
0
votes
2
replies
1.2k
views
Phyloseq to DESeq2
deseq2 phyloseq
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
1
reply
1.8k
views
Import_biom with tree problem
phyloseq mothur 16s
6.3 years ago andrebolerbarros ▴ 20
5
votes
11
replies
3.1k
views
Error while installing Phyloseq using biocLite
bioclite phyloseq install error
6.3 years ago khp ▴ 30
0
votes
9
replies
2.8k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
6.4 years ago eoin • 0
0
votes
1
reply
1.1k
views
Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
0
votes
1
reply
2.0k
views
Install package phyloseq
installation phyloseq
updated 6.9 years ago by 25k • written 6.9 years ago by • 0
0
votes
1
reply
1.9k
views
tip_glom and annotations?
ggtree treeio phyloseq annotation tip_glom
updated 7.0 years ago by ★ 1.2k • written 7.0 years ago by • 0
1
vote
1
reply
1.6k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
1
vote
8
replies
6.7k
views
Cannot read Biom file
r biomformat phyloseq
updated 7.2 years ago by ★ 1.0k • written 7.3 years ago by • 0
0
votes
0
replies
1.6k
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq installation ade4 macos
7.3 years ago sprague • 0
3
votes
2
replies
3.9k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
votes
1
reply
1.6k
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 7.4 years ago by ★ 13k • written 7.4 years ago by • 0
1
vote
3
replies
2.2k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
7.5 years ago lauren.czaplicki • 0
0
votes
1
reply
1.8k
views
Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 7.5 years ago by 43k • written 7.6 years ago by • 0
0
votes
0
replies
1.5k
views
Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
7.8 years ago David ▴ 860
1
vote
1
reply
4.0k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
7.8 years ago stats134711 • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Restricting differential binding analysis to only TSS-proximal regions by Aaron Lun ★ 28k
Seems reasonable to filter out windows outside of the TSS if you don't care about those events. IIRC the `discard` option will ignore any f…
Comment: Sample-specific methylation values using QSEA by User3088 • 0
Thanks Simon. I got the sample-specific methylation values by using '**samples=getSampleNames**' ``` result=makeTable(qs=prad_QSEAset, glm=…
Comment: input for singR function by iamin053 • 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Comment: build samplesheet and plot profile by yf • 0
![enter image description here][1] [1]: /media/images/8ea93bd0-bc90-443d-a332-4701f54a
Answer: I am having issues with bowtie2_build by James W. MacDonald 67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Votes
Unused arguments error without used arguments in GSVA?
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
A: Doubt about the "zero expression" genes or genes with no reads at all in the co
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
Awards • All
Popular Question to shepherl 4.1k
Popular Question to Gordon Smyth 52k
Popular Question to bastien_chassagnol • 0
Popular Question to Maria Doyle ▴ 100
Popular Question to Robert Ivanek ▴ 750
Locations • All
Pittsburgh, United States, just now
India, 19 minutes ago
EMBL Heidelberg, 23 minutes ago
United States, 1 hour ago
Australia, 1 hour ago
Traffic: 875 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6