Showing : Microbiome • reset
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727
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 7 months ago by 68k • written 7 months ago by • 0
0
votes
3
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1.5k
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 10 months ago by • 0 • written 23 months ago by • 0
1
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1
reply
487
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 12 months ago by ▴ 40 • written 12 months ago by ★ 1.6k
0
votes
2
replies
960
views
DESeq2 for microbiome data: raw counts or percentages?
microbiome DESeq2
18 months ago anton.kratz ▴ 60
2
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1
reply
2.1k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 20 months ago by ★ 4.8k • written 20 months ago by ▴ 10
0
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0
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706
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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
21 months ago Mohamed ▴ 30
0
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2
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2.6k
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stat_compare_means function - Error 'must have same length'
microbiomeDataSets Microbiome
2.3 years ago Elif • 0
1
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0
replies
757
views
News: Virtual talk “Model Misspecification in Microbiome Studies” by Amy D Willis
MicrobiomeData Microbiome
2.4 years ago Levi Waldron ★ 1.1k
1
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3
replies
8.8k
views
DESeq2 - Error: full model matrix is less than full rank
microbiome DESeq2
updated 2.6 years ago by ▴ 40 • written 4.6 years ago by • 0
0
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1
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1.1k
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
TreeSummarizedExperiment phylogenetic microbiome SummarizedExperiment
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
0
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3
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2.5k
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I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 2.8 years ago by 700 • written 2.8 years ago by • 0
2
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1
reply
2.6k
views
Deseq2 for 16s Data
Microbiome 16s Deseq2 16srRNA
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 10
0
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1
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1.1k
views
DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
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1
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811
views
pairwise within sample
DESeq2 microbiome
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
0
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1
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1.3k
views
Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData microbiome offtopic
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
0
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1
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1.2k
views
Adding insect abundance data to SparCC Analysis
sparcc Microbiome microbiomeExplorer MicrobiomeData
updated 3.9 years ago by ★ 4.0k • written 3.9 years ago by • 0
0
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0
replies
1.3k
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
3.9 years ago GlycineMax • 0
0
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0
replies
1.3k
views
News: Early career researchers: nominate to present your work at BVCN virtual conference on microbiome research
microbiome news Conference
4.3 years ago Matthew Ritchie ▴ 1000
0
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2
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1.5k
views
Question: export edgeR normalised OTU table
microbiome edgeR
4.3 years ago Pozdrawiam • 0
0
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2
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2.3k
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2 microbiome R
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
0
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1
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1.5k
views
MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 5.1 years ago by • 0 • written 8.4 years ago by • 0
0
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2
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1.1k
views
DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2 16s microbiome
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
0
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0
replies
1.2k
views
Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
5.4 years ago lhuang7 ▴ 50
1
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0
replies
1.1k
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
5.6 years ago supindab ▴ 10
0
votes
2
replies
1.7k
views
DESeq2 error on analyzing microbiome data
deseq2 microbiome sequencing
5.9 years ago • updated 5.8 years ago zhigang.li • 0
0
votes
2
replies
1.9k
views
DESeq2 Interaction Term Interpretation for Microbiome Data
deseq2 microbiome
updated 5.9 years ago by ★ 1.4k • written 5.9 years ago by • 0
0
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0
replies
1.2k
views
Aldex2 feature request - controlling for additional variables
ALDEx2 ALDEx microbiome 16s
6.4 years ago mstagliamonte ▴ 10
0
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1
reply
1.4k
views
metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
6.4 years ago slizo001 • 0
2
votes
1
reply
1.4k
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 6.5 years ago by ★ 3.6k • written 6.5 years ago by ▴ 870
0
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1
reply
1.3k
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
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1
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1.9k
views
DeSeq2 for comparison of experimental factors on microbial composition
deseq2 microbiome fungi fungal microbiome
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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0
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1.7k
views
Job: EXTENDED: Bioinformatics Specialist at the University of Illinois
microbiome epigenomics bioinformatics analyst NGS Job
7.1 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
1.6k
views
Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
7.3 years ago Jenny Drnevich ★ 2.0k
1
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1
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1.7k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
1
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1
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2.1k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 7.5 years ago by ▴ 280 • written 7.5 years ago by ▴ 10
3
votes
2
replies
4.1k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
0
votes
6
replies
1.9k
views
Why DESeq2 gives large logfold for group with all zero count?
microbiome 16s deseq2 differential gene expression
7.9 years ago lanhuong ▴ 20
0
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3
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2.0k
views
Where to find open access microbiome data for case-control comparative study?
microbiome data analysis data request
updated 8.1 years ago by ★ 13k • written 8.1 years ago by • 0
1
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1
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4.2k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
8.1 years ago stats134711 • 0
0
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2
replies
1.8k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
8.5 years ago Brian Smith ▴ 120
8
votes
1
reply
4.2k
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 8.6 years ago by ★ 13k • written 8.6 years ago by ▴ 30
0
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5
replies
4.0k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 8.7 years ago by ▴ 280 • written 8.7 years ago by • 0
0
votes
8
replies
3.8k
views
Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data
Microbiome DESeq2 Microbiome DESeq2
updated 8.8 years ago by ★ 13k • written 11.5 years ago by 43k
0
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0
replies
1.5k
views
Job: 2 year bioinformatics postdoc in the microbiome and prostate cancer risk @ UEA, Norwich, UK
Cancer microbiome postdoc UK prostate cancer Job
8.8 years ago Daniel Brewer ▴ 100
4
votes
3
replies
2.4k
views
Analyzing microbiome data (many zero-counts) using DESeq2
DESeq2 microbiome zero-inflated
updated 8.9 years ago by 43k • written 8.9 years ago by • 0
0
votes
5
replies
1.9k
views
deseq2 analysis, accounting for pen effect
deseq2 microbiome
updated 9.5 years ago by ★ 13k • written 9.5 years ago by ▴ 10
2
votes
1
reply
2.1k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2 differential expression microbiome
updated 9.7 years ago by 43k • written 9.7 years ago by • 0
1
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2
replies
2.2k
views
Normalization factors in metagenomeSeq
microbiome
10.1 years ago jovel_juan ▴ 30
2
votes
4
replies
2.8k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 2.4 years ago by • 0 • written 10.3 years ago by ▴ 30
1
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1
reply
3.5k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 10.3 years ago by ▴ 280 • written 10.3 years ago by ▴ 30
50 results • Page 1 of 1
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Comment: Check removeBatchEffect effectiveness by Gordon Smyth 52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
Comment: DiffBind - question on the use of filtered or unfiltered input data by sloperun3az • 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash by sloperun3az • 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr by Paul Harrison ▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
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Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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