Showing : microbiome • reset
0
votes
3
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976
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 12 days ago by • 0 • written 13 months ago by • 0
1
vote
1
reply
220
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 3 months ago by ▴ 40 • written 3 months ago by ★ 1.5k
0
votes
2
replies
616
views
DESeq2 for microbiome data: raw counts or percentages?
microbiome DESeq2
8 months ago anton.kratz ▴ 60
2
votes
1
reply
1.3k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 10 months ago by ★ 4.2k • written 10 months ago by ▴ 10
0
votes
0
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460
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Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics metagenomeSeq microbiome phyloseq microbiomeDataSets
11 months ago Mohamed ▴ 30
0
votes
2
replies
1.6k
views
stat_compare_means function - Error 'must have same length'
microbiomeDataSets Microbiome
17 months ago Elif • 0
1
vote
0
replies
567
views
News: Virtual talk “Model Misspecification in Microbiome Studies” by Amy D Willis
MicrobiomeData Microbiome
19 months ago Levi Waldron ★ 1.1k
1
vote
3
replies
7.4k
views
DESeq2 - Error: full model matrix is less than full rank
microbiome DESeq2
updated 22 months ago by ▴ 30 • written 3.8 years ago by • 0
0
votes
1
reply
810
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
TreeSummarizedExperiment phylogenetic microbiome SummarizedExperiment
updated 22 months ago by 66k • written 22 months ago by • 0
0
votes
3
replies
1.8k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 23 months ago by 700 • written 23 months ago by • 0
2
votes
1
reply
1.9k
views
Deseq2 for 16s Data
Microbiome 16s Deseq2 16srRNA
updated 2.3 years ago by 42k • written 2.3 years ago by ▴ 10
0
votes
1
reply
906
views
DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 2.5 years ago by 42k • written 2.5 years ago by • 0
0
votes
1
reply
639
views
pairwise within sample
DESeq2 microbiome
updated 2.9 years ago by 42k • written 2.9 years ago by • 0
0
votes
1
reply
997
views
Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData microbiome offtopic
updated 3.0 years ago by 66k • written 3.0 years ago by • 0
0
votes
1
reply
955
views
Adding insect abundance data to SparCC Analysis
sparcc Microbiome microbiomeExplorer MicrobiomeData
updated 3.1 years ago by ★ 4.0k • written 3.1 years ago by • 0
0
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0
replies
1.1k
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
3.1 years ago GlycineMax • 0
0
votes
0
replies
1.1k
views
News: Early career researchers: nominate to present your work at BVCN virtual conference on microbiome research
microbiome news Conference
3.5 years ago Matthew Ritchie ▴ 1000
0
votes
2
replies
1.3k
views
Question: export edgeR normalised OTU table
microbiome edgeR
3.5 years ago Pozdrawiam • 0
0
votes
2
replies
1.8k
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2 microbiome R
updated 3.9 years ago by 42k • written 3.9 years ago by • 0
0
votes
1
reply
1.3k
views
MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 4.3 years ago by • 0 • written 7.6 years ago by • 0
0
votes
2
replies
934
views
DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2 16s microbiome
updated 4.5 years ago by 42k • written 4.5 years ago by ▴ 10
0
votes
0
replies
1000
views
Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
4.6 years ago lhuang7 ▴ 50
1
vote
0
replies
940
views
Job: Bioinformatician: NEW YORK CITY - Institute for Data Science and Genomic Technology, Mount Sinai School of Medicine
job bioinformatician systems biology microbiome genomics Job
4.8 years ago supindab ▴ 10
0
votes
2
replies
1.4k
views
DESeq2 error on analyzing microbiome data
deseq2 microbiome sequencing
5.0 years ago zhigang.li • 0
0
votes
2
replies
1.6k
views
DESeq2 Interaction Term Interpretation for Microbiome Data
deseq2 microbiome
updated 5.1 years ago by ★ 1.4k • written 5.1 years ago by • 0
0
votes
0
replies
963
views
Aldex2 feature request - controlling for additional variables
ALDEx2 ALDEx microbiome 16s
5.6 years ago mstagliamonte ▴ 10
0
votes
1
reply
1.2k
views
metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
5.6 years ago slizo001 • 0
2
votes
1
reply
1.2k
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 5.7 years ago by ★ 3.6k • written 5.7 years ago by ▴ 850
0
votes
1
reply
1.1k
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 5.7 years ago by 42k • written 5.7 years ago by • 0
0
votes
1
reply
1.7k
views
DeSeq2 for comparison of experimental factors on microbial composition
deseq2 microbiome fungi fungal microbiome
updated 6.2 years ago by 42k • written 6.2 years ago by • 0
0
votes
0
replies
1.4k
views
Job: EXTENDED: Bioinformatics Specialist at the University of Illinois
microbiome epigenomics bioinformatics analyst NGS Job
6.3 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
1.3k
views
Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
6.5 years ago Jenny Drnevich ★ 2.0k
1
vote
1
reply
1.5k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 6.7 years ago by 42k • written 6.7 years ago by • 0
1
vote
1
reply
1.9k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 6.7 years ago by ▴ 280 • written 6.7 years ago by ▴ 10
3
votes
2
replies
3.5k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 6.9 years ago by 42k • written 6.9 years ago by • 0
0
votes
6
replies
1.7k
views
Why DESeq2 gives large logfold for group with all zero count?
microbiome 16s deseq2 differential gene expression
7.1 years ago lanhuong ▴ 20
0
votes
3
replies
1.7k
views
Where to find open access microbiome data for case-control comparative study?
microbiome data analysis data request
updated 7.3 years ago by ★ 13k • written 7.3 years ago by • 0
1
vote
1
reply
3.7k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
7.3 years ago stats134711 • 0
0
votes
2
replies
1.6k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
7.7 years ago Brian Smith ▴ 120
6
votes
1
reply
3.4k
views
Using R package 'limma' on pre-normalized counts and the effect of non-equivalent reads/sample on limma linear model
limma rna-seq multi-mapped reads normalization microbiome
updated 7.8 years ago by ★ 13k • written 7.8 years ago by ▴ 20
0
votes
5
replies
3.7k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 7.9 years ago by ▴ 280 • written 7.9 years ago by • 0
0
votes
8
replies
3.4k
views
Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data
Microbiome DESeq2 Microbiome DESeq2
updated 7.9 years ago by ★ 13k • written 10.7 years ago by 42k
0
votes
0
replies
1.4k
views
Job: 2 year bioinformatics postdoc in the microbiome and prostate cancer risk @ UEA, Norwich, UK
Cancer microbiome postdoc UK prostate cancer Job
8.0 years ago Daniel Brewer ▴ 100
4
votes
3
replies
2.1k
views
Analyzing microbiome data (many zero-counts) using DESeq2
DESeq2 microbiome zero-inflated
updated 8.1 years ago by 42k • written 8.1 years ago by • 0
0
votes
5
replies
1.6k
views
deseq2 analysis, accounting for pen effect
deseq2 microbiome
updated 8.7 years ago by ★ 13k • written 8.7 years ago by ▴ 10
2
votes
1
reply
1.9k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2 differential expression microbiome
updated 8.9 years ago by 42k • written 8.9 years ago by • 0
1
vote
2
replies
2.0k
views
Normalization factors in metagenomeSeq
microbiome
9.3 years ago jovel_juan ▴ 30
2
votes
4
replies
2.4k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 19 months ago by • 0 • written 9.5 years ago by ▴ 30
1
vote
1
reply
3.1k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 9.5 years ago by ▴ 280 • written 9.5 years ago by ▴ 30
1
vote
1
reply
1.7k
views
Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 9.5 years ago by ▴ 280 • written 9.5 years ago by ▴ 30
50 results • Page 1 of 1
Recent ...
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Comment: 'path' must be string by James W. MacDonald 66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string by cpierce2 • 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest by Robert • 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta by Guido Hooiveld ★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta by Michael Love 42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
Awards • All
Popular Question to Lluís Revilla Sancho ▴ 730
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Scholar to Michael Love 42k
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Scholar to Gordon Smyth 51k
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