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2
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221
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How to retrieve detailed regression results from deseq2
DESeq2
15 days ago • updated 6 days ago
Weiqian
▴ 10
1
vote
0
replies
208
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
7 days ago • updated 6 days ago
BioinfGuru
▴ 30
0
votes
7
replies
389
views
DESeq filtering specific to contrasts
DESeq2
updated 6 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
25 days ago • updated 7 days ago
isaac.vock
• 0
0
votes
3
replies
103
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 7 days ago by
James W. MacDonald
65k • written 7 days ago by
bas_work
▴ 30
2
votes
5
replies
700
views
DESeq2 setting significant p-value
DESeq2
updated 7 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
2
votes
2
replies
143
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 7 days ago by
James W. MacDonald
65k • written 7 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 7 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
0
votes
4
replies
231
views
DEG with low counts
DESeq2
updated 7 days ago by
Michael Love
41k • written 11 days ago by
Rajat
• 0
6
votes
5
replies
398
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 8 weeks ago by
Kim
• 0
0
votes
3
replies
130
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 7 days ago by
Gordon Smyth
50k • written 7 days ago by
prity6459
• 0
0
votes
2
replies
91
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
7 days ago
prity6459
• 0
3
votes
1
reply
121
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 7 days ago by
Gordon Smyth
50k • written 8 days ago by
Shaimaa Gamal
• 0
0
votes
2
replies
901
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
4
votes
8
replies
352
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 7 days ago by
Peter Hickey
▴ 740 • written 15 days ago by
Juan Higareda
• 0
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 7 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
0
votes
4
replies
135
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
7 days ago
sropri
• 0
1
vote
2
replies
183
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
8 days ago • updated 7 days ago
Le
• 0
0
votes
3
replies
227
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 7 days ago by
W. Evan Johnson
▴ 850 • written 14 days ago by
schlumbohm
• 0
0
votes
0
replies
88
views
Warning while loading DEP package
DEP
updated 7 days ago by
shepherl
3.8k • written 7 days ago by
Namrata
• 0
0
votes
1
reply
86
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 7 days ago by
Alejandro Reyes
★ 1.9k • written 8 days ago by
Alessia
• 0
0
votes
1
reply
120
views
Adding columns to DEXSeqResults object
DEXSeq
updated 7 days ago by
Alejandro Reyes
★ 1.9k • written 9 days ago by
Clyde
• 0
0
votes
1
reply
92
views
rlog transformation
DESeq2
updated 7 days ago by
Michael Love
41k • written 8 days ago by
ishij9717
• 0
0
votes
1
reply
90
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 7 days ago by
Michael Love
41k • written 8 days ago by
09191919
• 0
0
votes
1
reply
115
views
covariate with negative and positive values
DESeq2
updated 7 days ago by
Michael Love
41k • written 9 days ago by
Brynn
• 0
1
vote
2
replies
124
views
Error in champ.load(): The following specified files do not exist
ChAMP
8 days ago
Sherin
• 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 8 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
5
votes
9
replies
860
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
15 days ago • updated 8 days ago
Chris
• 0
0
votes
1
reply
80
views
Input Question for deseq.r
RSeqAn
updated 8 days ago by
ATpoint
★ 4.0k • written 8 days ago by
Nina
• 0
0
votes
1
reply
121
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 8 days ago by
ATpoint
★ 4.0k • written 9 days ago by
quanah.hudson
• 0
3
votes
3
replies
175
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
14 days ago • updated 8 days ago
jacques.imbert
• 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 8 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 8 days ago
shepherl
3.8k
0
votes
2
replies
890
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 8 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 9 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 9 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
0
votes
0
replies
64
views
News:
Services
flowBeads
9 days ago
creativepeptides2018
• 0
0
votes
0
replies
58
views
Enzyme Engineering
BioTIP
9 days ago
bocchemistry
• 0
0
votes
0
replies
62
views
News:
TIDES USA 2024
flowBeads
9 days ago
bocsci11
• 0
0
votes
0
replies
79
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
9 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 9 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
4
replies
155
views
flowStats Search Error
flowStats
updated 9 days ago by
shepherl
3.8k • written 10 days ago by
tholmes
• 0
0
votes
1
reply
119
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 9 days ago by
James W. MacDonald
65k • written 12 days ago by
tian.liu0720
• 0
1
vote
2
replies
113
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
9 days ago
Ana
• 0
0
votes
1
reply
101
views
what is the sampleFiles
chipseq
updated 10 days ago by
James W. MacDonald
65k • written 10 days ago by
zhulin
• 0
0
votes
3
replies
176
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 10 days ago by
Michael Love
41k • written 11 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
162
views
Differentially expressed genes in monocle pseudotime
monocle
updated 10 days ago by
Gordon Smyth
50k • written 12 days ago by
kthapa
• 0
2
votes
2
replies
149
views
[DiffBind] Obtaining normalization factors
DiffBind
13 days ago • updated 10 days ago
Henry
▴ 10
2
votes
3
replies
295
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
11 days ago • updated 10 days ago
daniel.carbajo
• 0
202 results • Page
2 of 5
Recent ...
Replies
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
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…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
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…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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