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1
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2
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222
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How to retrieve detailed regression results from deseq2
DESeq2
16 days ago • updated 7 days ago
Weiqian
▴ 10
1
vote
0
replies
209
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
8 days ago • updated 7 days ago
BioinfGuru
▴ 30
0
votes
7
replies
391
views
DESeq filtering specific to contrasts
DESeq2
updated 8 days ago by
Michael Love
41k • written 10 weeks ago by
Emma
• 0
0
votes
2
replies
238
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
26 days ago • updated 8 days ago
isaac.vock
• 0
0
votes
3
replies
105
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
bas_work
▴ 30
2
votes
5
replies
705
views
DESeq2 setting significant p-value
DESeq2
updated 8 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
2
votes
2
replies
145
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
sansan
• 0
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 8 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
0
votes
4
replies
236
views
DEG with low counts
DESeq2
updated 8 days ago by
Michael Love
41k • written 12 days ago by
Rajat
• 0
6
votes
5
replies
399
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 8 weeks ago by
Kim
• 0
0
votes
3
replies
135
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 8 days ago by
Gordon Smyth
50k • written 8 days ago by
prity6459
• 0
0
votes
2
replies
93
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
8 days ago
prity6459
• 0
3
votes
1
reply
127
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 8 days ago by
Gordon Smyth
50k • written 9 days ago by
Shaimaa Gamal
• 0
0
votes
2
replies
904
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
4
votes
8
replies
360
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 8 days ago by
Peter Hickey
▴ 740 • written 16 days ago by
Juan Higareda
• 0
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 8 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
0
votes
4
replies
142
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
8 days ago
sropri
• 0
1
vote
2
replies
191
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
9 days ago • updated 8 days ago
Le
• 0
0
votes
3
replies
232
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 8 days ago by
W. Evan Johnson
▴ 850 • written 15 days ago by
schlumbohm
• 0
0
votes
0
replies
91
views
Warning while loading DEP package
DEP
updated 9 days ago by
shepherl
3.8k • written 9 days ago by
Namrata
• 0
0
votes
1
reply
91
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 9 days ago by
Alejandro Reyes
★ 1.9k • written 9 days ago by
Alessia
• 0
0
votes
1
reply
124
views
Adding columns to DEXSeqResults object
DEXSeq
updated 9 days ago by
Alejandro Reyes
★ 1.9k • written 10 days ago by
Clyde
• 0
0
votes
1
reply
98
views
rlog transformation
DESeq2
updated 9 days ago by
Michael Love
41k • written 9 days ago by
ishij9717
• 0
0
votes
1
reply
92
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 9 days ago by
Michael Love
41k • written 9 days ago by
09191919
• 0
0
votes
1
reply
117
views
covariate with negative and positive values
DESeq2
updated 9 days ago by
Michael Love
41k • written 10 days ago by
Brynn
• 0
1
vote
2
replies
129
views
Error in champ.load(): The following specified files do not exist
ChAMP
9 days ago
Sherin
• 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 9 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
5
votes
9
replies
868
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
16 days ago • updated 9 days ago
Chris
• 0
0
votes
1
reply
82
views
Input Question for deseq.r
RSeqAn
updated 9 days ago by
ATpoint
★ 4.0k • written 9 days ago by
Nina
• 0
0
votes
1
reply
123
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 9 days ago by
ATpoint
★ 4.0k • written 10 days ago by
quanah.hudson
• 0
3
votes
3
replies
178
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
15 days ago • updated 9 days ago
jacques.imbert
• 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 9 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
3
votes
18
replies
2.9k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 9 days ago
shepherl
3.8k
0
votes
2
replies
891
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 9 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP
EPICv2
updated 10 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 10 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
0
votes
0
replies
64
views
News:
Services
flowBeads
10 days ago
creativepeptides2018
• 0
0
votes
0
replies
60
views
Enzyme Engineering
BioTIP
10 days ago
bocchemistry
• 0
0
votes
0
replies
64
views
News:
TIDES USA 2024
flowBeads
10 days ago
bocsci11
• 0
0
votes
0
replies
80
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
10 days ago
Maliha Tabassum
• 0
0
votes
4
replies
573
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 10 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
4
replies
158
views
flowStats Search Error
flowStats
updated 10 days ago by
shepherl
3.8k • written 11 days ago by
tholmes
• 0
0
votes
1
reply
121
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 10 days ago by
James W. MacDonald
65k • written 13 days ago by
tian.liu0720
• 0
1
vote
2
replies
115
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
11 days ago
Ana
• 0
0
votes
1
reply
103
views
what is the sampleFiles
chipseq
updated 11 days ago by
James W. MacDonald
65k • written 11 days ago by
zhulin
• 0
0
votes
3
replies
177
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 11 days ago by
Michael Love
41k • written 12 days ago by
andrebolerbarros
▴ 20
0
votes
5
replies
1.6k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
1
vote
1
reply
166
views
Differentially expressed genes in monocle pseudotime
monocle
updated 11 days ago by
Gordon Smyth
50k • written 13 days ago by
kthapa
• 0
2
votes
2
replies
151
views
[DiffBind] Obtaining normalization factors
DiffBind
15 days ago • updated 11 days ago
Henry
▴ 10
2
votes
3
replies
298
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
12 days ago • updated 11 days ago
daniel.carbajo
• 0
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Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
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1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
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pl23
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Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
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For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
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Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
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Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
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Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
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