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DESeq2
•
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0
votes
0
replies
15
views
DEseq2 to test half-life for time-series data
half-life
DESeq2
time-series
7 hours ago
Xianjun Dong
• 0
0
votes
2
replies
41
views
Outliers
outliers
Deseq2
1 day ago • updated 22 hours ago
nolwenn
• 0
3
votes
3
replies
77
views
Query regarding Differential gene expression analysis
limma
edgeR
DESeq2
2 days ago • updated 1 day ago
abhisekdey061
• 0
0
votes
9
replies
250
views
How to setup sample design in DESeq2
DESeq2
6 weeks ago • updated 1 day ago
dequattro.concetta
▴ 10
0
votes
0
replies
33
views
Range value of the dispersion parameters (a1, alpha 0 and sigmad)
dispersion
DESeq2
polyester
2 days ago
catalina.gonzalez-gomez
• 0
1
vote
12
replies
134
views
Data normalization
DESeq2
Normalization
2 days ago • updated 1 day ago
nolwenn
• 0
0
votes
1
reply
35
views
Deseq2 error "Error in designAndArgChecker"
DESeq2
updated 2 days ago by
Michael Love
32k • written 3 days ago by
polaxgr
▴ 10
1
vote
2
replies
46
views
Different genes using same method
DESeq2
3 days ago
menuka
• 0
1
vote
3
replies
109
views
Preferential sequencing of longer Genes in Illumina?
DESeq2
sequencing
updated 12 days ago by
victorbradford4
• 0 • written 13 days ago by
simplyphage
• 0
2
votes
2
replies
103
views
is the P value reliable if the counts are Low across the sample ?
DESeq2
sequencing
14 days ago
simplyphage
• 0
2
votes
2
replies
123
views
How to reassign DESeqDataSet design to include newly added column to columnData
DESeq2
14 days ago
rnavabjj
• 0
0
votes
1
reply
64
views
DEseq2 for analysis of time points
DESeq2
timepoints
updated 14 days ago by
Kevin Blighe
2.7k • written 15 days ago by
Chloe
• 0
2
votes
3
replies
88
views
DESEQ2: Some genes have empty pvalue and padj
DESeq2
updated 15 days ago by
ATpoint
▴ 570 • written 15 days ago by
Bine
▴ 10
0
votes
2
replies
79
views
Comparison when Control is in differen batch
DESeq2
DifferentialExpression
updated 15 days ago by
Kevin Blighe
2.7k • written 15 days ago by
rina
• 0
0
votes
2
replies
80
views
Deseq2 cooks filter for 2 replicates x 3 replicates
DESeq2
Nullcook'svalues
2x3
DEGs
15 days ago
andreia
• 0
1
vote
2
replies
74
views
Biological Replicate factor in Design Formula (DESeq2)
DESeq2
16 days ago • updated 15 days ago
DcL-A
• 0
0
votes
1
reply
61
views
Wald or LR Test
DESeq2
DifferentialExpression
updated 17 days ago by
Michael Love
32k • written 17 days ago by
Matt
• 0
0
votes
3
replies
83
views
DESeq2 - extracting results - Gnomon gene model
DESeq2
Gnomon
Biostrings
17 days ago • updated 7 days ago
sieminsk
• 0
4
votes
18
replies
434
views
DESeq2 - multifactorial design
LRT
DESeq2
interaction
updated 16 days ago by
Kevin Blighe
2.7k • written 4 weeks ago by
annamariabugaj
▴ 10
0
votes
4
replies
152
views
How sensitive is DiffBind to Deseq2 assumptions ?
DESeq2
DiffBind
updated 3 days ago by
Rory Stark
★ 3.8k • written 20 days ago by
Sam
▴ 10
0
votes
1
reply
58
views
DESEQ2 normalization for time series data
DESeq2
Normalization
Medianofratios
updated 21 days ago by
Michael Love
32k • written 21 days ago by
Joshua
• 0
0
votes
2
replies
93
views
Using a numeric contrast vector to find genes differentially expressed by non-additive effect of a condition
DESeq2
written 22 days ago by
TJ
• 0
2
votes
4
replies
165
views
DESEQ2 Formula with 5 variables
DESeq2
22 days ago • updated 20 days ago
Bine
▴ 10
3
votes
3
replies
124
views
DESEQ object filter
DESeq2
written 23 days ago by
Bine
▴ 10
1
vote
1
reply
50
views
DESeq2 Installation fails with non-zero exit status
DESeq2
updated 23 days ago by
Michael Love
32k • written 23 days ago by
wlorenz
• 0
2
votes
2
replies
61
views
TxImport when quant.sf files have different index files
tximport
DESeq2
23 days ago
mprnl
• 0
0
votes
4
replies
82
views
Problem install: Package ‘DESeq2’ is not available for this version of R
DESeq2
updated 23 days ago by
ATpoint
▴ 570 • written 23 days ago by
reneclassens92
• 0
0
votes
4
replies
74
views
replaceOutliers in DESeq2 : need to recompute size Factors ?
DESeq2
24 days ago • updated 23 days ago
eleonoregravier
▴ 60
3
votes
2
replies
92
views
DeSeq2 design for sgRNA fold-change
DESeq2
updated 24 days ago by
Michael Love
32k • written 24 days ago by
P1000
• 0
2
votes
3
replies
77
views
Failing to install DESeq because the version is not compatible
DESeq2
updated 23 days ago by
shepherl
2.6k • written 24 days ago by
Evy_00
• 0
0
votes
1
reply
58
views
Non-significant but high LFC after apeglm shrinkage
DESeq2
apeglm
updated 24 days ago by
Michael Love
32k • written 24 days ago by
hpapoli
• 0
1
vote
3
replies
74
views
DEGpatterns and functional analysis of clusters
DESeq2
RNASeq
DEGreport
updated 24 days ago by
Kevin Blighe
2.7k • written 25 days ago by
Giulia
• 0
3
votes
5
replies
109
views
Cook's distance outlier detection
DESeq2
cook'sdistance
25 days ago • updated 24 days ago
hpapoli
• 0
2
votes
1
reply
109
views
DESeq2 fold change filtering
DESeq2
updated 25 days ago by
Michael Love
32k • written 26 days ago by
zao.liun95
▴ 10
1
vote
4
replies
140
views
DESeq2 - How can we correct for a "Group-specific condition effect" if the condition can be applied to one group only?
DESeq2
27 days ago • updated 25 days ago
Tamer
▴ 10
5
votes
4
replies
130
views
Using DESeq2 with GlmGamPoi
DESeq2
glmGamPoi
scRNAseq
26 days ago • updated 24 days ago
tatyana.perlova
• 0
2
votes
5
replies
140
views
DESeq2: relevel() unsuccessfully setting control group
DESeq2
updated 26 days ago by
hanumwijayanty
• 0 • written 28 days ago by
vanbelj
▴ 10
0
votes
1
reply
72
views
Metatranscriptomics DESeq2 multifactorial sampling
Transcriptomics
DESeq2
updated 28 days ago by
Michael Love
32k • written 28 days ago by
seppe.demits
• 0
0
votes
2
replies
69
views
Finding the correct version of DESeq2 for my version of R (3.6.1)
error
DESeq2
Install
updated 28 days ago by
James W. MacDonald
56k • written 28 days ago by
Mick
• 0
0
votes
4
replies
136
views
How to use combat in order to remove batch effects?
BatchEffect
DESeq2
RNASeqData
written 29 days ago by
Emma
• 0
0
votes
1
reply
45
views
How to analyze ribosome profiling data in the form of a 2x2x2 experiment using DESeq2
DESeq2
RiboSeq
RNASeq
updated 29 days ago by
Michael Love
32k • written 29 days ago by
kyusikkim
• 0
1
vote
3
replies
101
views
Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2
RNA-seq
updated 29 days ago by
Michael Love
32k • written 4 weeks ago by
zroger499
• 0
0
votes
3
replies
121
views
DESeq2: Too many "NA" for adjPvalue
DESeq2
updated 29 days ago by
Michael Love
32k • written 4 weeks ago by
sagharib
• 0
0
votes
1
reply
88
views
is docker image using DESeq portable?
bioconductor/bioconductor_docker
DESeq2
updated 4 weeks ago by
nitesh.turaga
140 • written 4 weeks ago by
aedavids
• 0
5
votes
6
replies
222
views
DESeq2 / PCA Analysis of RNA-seq Data - Best Explanatory Resource?
DESeq2
pcaExplorer
updated 4 weeks ago by
Michael Love
32k • written 4 weeks ago by
vanbelj
▴ 10
2
votes
2
replies
90
views
Negative svalues from DESeq2 lfcShrink with ashr
ashr
DESeq2
lfcShrink
svalue
4 weeks ago
Enrico
• 0
0
votes
1
reply
78
views
DESeq2 calling DEGs despite detection in few replicates
DESeq2
updated 4 weeks ago by
swbarnes2
▴ 670 • written 4 weeks ago by
lnblock2
• 0
0
votes
2
replies
147
views
DESeq2 design formula and batch correction
DESeq2
updated 4 weeks ago by
Michael Love
32k • written 5 weeks ago by
lransom
• 0
0
votes
3
replies
141
views
Understanding MA plot distortion
DESeq2
MAplot
deseq
updated 4 weeks ago by
Michael Love
32k • written 4 weeks ago by
sp
• 0
1
vote
4
replies
161
views
An attempt to better understand DESeq2 dispersion estimation
DESeq2
5 weeks ago • updated 24 days ago
Sam
▴ 10
3,374 results • Page
1 of 68
Recent ...
Replies
Answer: Differential Transcript Usage: complex factorial design
by
Gordon Smyth
42k
edgeR does differential expression for transcripts via the catchSalmon function followed the usual edgeR pipelines as you would do for gene…
Comment: RSamtools idxstatsBam not working with remote bam file
by
mja18
▴ 30
Thanks Martin. Yes, that works.
Answer: RSamtools idxstatsBam not working with remote bam file
by
Martin Morgan
25k
Can you tell me if the following works for you? In a new R session ```{r} library(Rsamtools) setMethod(idxstatsBam, "BamFile", …
Comment: Aspli: error with gbCounts
by
achernomoretz
• 0
Hi Jeremy. We got it and we are working on the issue. Thanks for your patience. A
Comment: Aspli: error with gbCounts
by
jbono
• 0
Sorry, I forgot to respond here that I sent the file via email. Please let me know if you didn't receive it, thanks!
Votes
Answer: RSamtools idxstatsBam not working with remote bam file
Running > 100 samples per group - memory issues
R failing to load genome files from EnsDb.Hsapiens.v86
Comment: TCGA data analysis
Comment: BSGenome Forge for non-model organism
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