Showing : Microbiome • reset
0
votes
2
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76
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I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
3 days ago • updated 2 days ago kikiki • 0
1
vote
1
reply
235
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Deseq2 for 16s Data
Microbiome 16s Deseq2 16srRNA
updated 3 months ago by 37k • written 3 months ago by • 0
0
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1
reply
246
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DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 6 months ago by 37k • written 6 months ago by • 0
0
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1
reply
194
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pairwise within sample
DESeq2 microbiome
updated 11 months ago by 37k • written 11 months ago by • 0
0
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1
reply
273
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Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData microbiome offtopic
updated 12 months ago by 60k • written 12 months ago by • 0
0
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1
reply
333
views
Adding insect abundance data to SparCC Analysis
sparcc Microbiome microbiomeExplorer MicrobiomeData
updated 13 months ago by 3.6k • written 13 months ago by • 0
0
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0
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311
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Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
13 months ago GlycineMax • 0
0
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0
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453
views
News: Early career researchers: nominate to present your work at BVCN virtual conference on microbiome research
microbiome news Conference
18 months ago Matthew Ritchie ▴ 1000
0
votes
2
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522
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Question: export edgeR normalised OTU table
microbiome edgeR
18 months ago Pozdrawiam • 0
1
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2
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2.4k
views
DESeq2 - Error: full model matrix is less than full rank
microbiome DESeq2
21 months ago Daniel • 0
0
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2
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731
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Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2 microbiome R
updated 23 months ago by 37k • written 23 months ago by • 0
0
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1
reply
779
views
MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 2.3 years ago by • 0 • written 5.7 years ago by • 0
0
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2
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312
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DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2 16s microbiome
updated 2.5 years ago by 37k • written 2.5 years ago by • 0
0
votes
0
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464
views
Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
2.6 years ago lhuang7 ▴ 50
1
vote
0
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413
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
2.8 years ago supindab ▴ 10
0
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2
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573
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DESeq2 error on analyzing microbiome data
deseq2 microbiome sequencing
3.1 years ago zhigang.li • 0
0
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2
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630
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DESeq2 Interaction Term Interpretation for Microbiome Data
deseq2 microbiome
updated 3.1 years ago by ★ 1.1k • written 3.1 years ago by • 0
0
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0
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458
views
Aldex2 feature request - controlling for additional variables
ALDEx2 ALDEx microbiome 16s
3.6 years ago mstagliamonte • 0
0
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1
reply
567
views
metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
3.7 years ago slizo001 • 0
2
votes
1
reply
599
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 3.8 years ago by ★ 3.5k • written 3.8 years ago by ▴ 840
0
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1
reply
509
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 3.8 years ago by 37k • written 3.8 years ago by • 0
0
votes
1
reply
964
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DeSeq2 for comparison of experimental factors on microbial composition
deseq2 microbiome fungi fungal microbiome
updated 4.2 years ago by 37k • written 4.2 years ago by • 0
0
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0
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708
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Job: EXTENDED: Bioinformatics Specialist at the University of Illinois
microbiome epigenomics bioinformatics analyst NGS Job
4.4 years ago Jenny Drnevich ★ 2.0k
0
votes
0
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722
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Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
4.5 years ago Jenny Drnevich ★ 2.0k
1
vote
1
reply
852
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 4.7 years ago by 37k • written 4.7 years ago by • 0
1
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1
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1.0k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 4.7 years ago by ▴ 280 • written 4.7 years ago by ▴ 10
2
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2
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2.0k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 4.9 years ago by 37k • written 4.9 years ago by • 0
0
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6
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1.0k
views
Why DESeq2 gives large logfold for group with all zero count?
microbiome 16s deseq2 differential gene expression
5.2 years ago lanhuong ▴ 20
0
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3
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1.0k
views
Where to find open access microbiome data for case-control comparative study?
microbiome data analysis data request
updated 5.3 years ago by 13k • written 5.3 years ago by • 0
1
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1
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2.4k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
5.3 years ago stats134711 • 0
0
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2
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1.0k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
5.7 years ago Brian Smith ▴ 120
3
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1
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1.9k
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 5.8 years ago by 13k • written 5.8 years ago by • 0
0
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5
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2.6k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 5.9 years ago by ▴ 280 • written 5.9 years ago by • 0
0
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8
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2.5k
views
Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data
Microbiome DESeq2 Microbiome DESeq2
updated 6.0 years ago by 13k • written 8.7 years ago by 37k
0
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0
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879
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Job: 2 year bioinformatics postdoc in the microbiome and prostate cancer risk @ UEA, Norwich, UK
Cancer microbiome postdoc UK prostate cancer Job
6.0 years ago Daniel Brewer ▴ 90
4
votes
3
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1.4k
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Analyzing microbiome data (many zero-counts) using DESeq2
DESeq2 microbiome zero-inflated
updated 6.1 years ago by 37k • written 6.1 years ago by • 0
0
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5
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1.0k
views
deseq2 analysis, accounting for pen effect
deseq2 microbiome
updated 6.8 years ago by 13k • written 6.8 years ago by ▴ 10
2
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1
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1.4k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2 differential expression microbiome
updated 6.9 years ago by 37k • written 6.9 years ago by • 0
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2
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1.4k
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Normalization factors in metagenomeSeq
microbiome
7.3 years ago jovel_juan ▴ 10
2
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3
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1.6k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 7.5 years ago by ▴ 280 • written 7.5 years ago by ▴ 30
1
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1
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2.3k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 7.6 years ago by ▴ 280 • written 7.6 years ago by ▴ 30
1
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1
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1.1k
views
Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 7.6 years ago by ▴ 280 • written 7.6 years ago by ▴ 10
2
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2
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842
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no timeInterval output using fitTimeSeries
metagenomeSeq fitTimeSeries microbiome
7.6 years ago noelle.noyes ▴ 30
2
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2
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1.1k
views
error using fitTimeSeries from metagenomeSeq
metagenomeSeq microbiome
7.6 years ago noelle.noyes ▴ 30
1
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1
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1.3k
views
metagenomeSeq error using plotMRheatmap and display() heatmaps and PCA/MDS plots
metagenomseq microbiome
updated 7.6 years ago by ▴ 280 • written 7.6 years ago by ▴ 30
0
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1
reply
915
views
error with fitTimeSeries in metagenomeSeq" invalid 'times’ argument"
microbiome
updated 7.8 years ago by ▴ 280 • written 7.8 years ago by • 0
1
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2
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4.1k
views
DESeq2: What is the impact if glm.fit does not converge during rlogTransformation or varianceStabilizingTransformation
deseq2 normalization microbiome
updated 7.9 years ago by 37k • written 7.9 years ago by • 0
0
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3
replies
2.9k
views
phyloseq/DESeq gives negative transformed values
Microbiome Normalization Clustering DESeq DESeq2 Microbiome Normalization Clustering DESeq
updated 8.3 years ago by ▴ 130 • written 8.3 years ago by 37k
2
votes
19
replies
1.9k
views
phyloseq/DESeq gives negative transformed values
Microbiome DESeq Microbiome DESeq
updated 8.3 years ago by 37k • written 8.3 years ago by ▴ 130
0
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0
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2.2k
views
Pathview with non-KEGG organisms?
Microbiome Pathways GO Visualization Organism graph gage pathview Microbiome Pathways GO
9.0 years ago Luo Weijun ★ 1.5k
50 results • Page 1 of 1
Recent ...
Replies
Comment: Data input for aracne2regulon function in viper package by xlal • 0
You are right!And may be we should check the gene symbols cause when I open the expression matrix in EXCEL,it will change some genes into m…
Comment: unable to install.packages("spatialLIBD") by Leonardo Collado Torres ▴ 1000
All the solutions Lori proposed are valid. The `STexampleData` package I think has only 1 of our samples (see https://bioconductor.org/pack…
Answer: how to use Rsamtools to parse extra fields from STAR alignment by Martin Morgan 25k
The 'extra columns' are called 'tags' in the SAM specification. Following the documentation `?ScanBamParam` you should add `tag = "NH"`. Se…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip by Delta._.43 ▴ 10
Yes, indeed it is the same error. Here are the first few lines of my count file. ``` "ENSG00000000003":"001" 0 "ENSG00000000003":"002" 1032…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip by Alejandro Reyes ★ 1.8k
Thanks for your detail post. I think this might be related to this issue here: https://support.bioconductor.org/p/9143537/ Just to verify…
Votes
Answer: spot- vs cell-level data access
Answer: unable to install.packages("spatialLIBD")
Comment: unable to install.packages("spatialLIBD")
error running UniProt.ws
Answer: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FU
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