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Showing :
Deseq2
•
reset
1
vote
2
replies
119
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
6 days ago • updated 17 hours ago
Chanderkant Chaudhary
• 0
0
votes
3
replies
140
views
PCA of different bacterial species
DESeq2
updated 21 hours ago by
Michael Love
41k • written 1 day ago by
Laura
▴ 10
0
votes
7
replies
334
views
DESeq2 filtering vs edgeR filtering
DESeq2
14 days ago • updated 1 day ago
fr8712ca-s
• 0
0
votes
1
reply
81
views
collapseReplicates dimension error
DESeq2
Dese
updated 2 days ago by
Michael Love
41k • written 5 days ago by
Léa
• 0
3
votes
2
replies
111
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
2 days ago
Anita
▴ 10
0
votes
2
replies
131
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
7 days ago • updated 6 days ago
kcarey
• 0
1
vote
3
replies
220
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 7 days ago by
Michael Love
41k • written 9 days ago by
andrebolerbarros
▴ 20
0
votes
3
replies
175
views
Help with Complex DESeq2 Design
DESeq2
updated 8 days ago by
ATpoint
★ 4.0k • written 9 days ago by
kelsey.beavers
• 0
4
votes
7
replies
611
views
DESeq2 unable to handle large count values
DESeq2
updated 8 days ago by
Michael Love
41k • written 4 months ago by
robennet
• 0
1
vote
1
reply
119
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2
ctsGE
updated 9 days ago by
Michael Love
41k • written 10 days ago by
Emma
• 0
0
votes
1
reply
96
views
Help with DESeqDataSetFromHTSeqCount
DESeq2
RSeqAn
updated 9 days ago by
Michael Love
41k • written 9 days ago by
rahaf.nazzal9
• 0
0
votes
1
reply
114
views
lfcShrink error: the line search routine failed
apeglm
DESeq2
updated 10 days ago by
Michael Love
41k • written 10 days ago by
Yuqin
• 0
2
votes
2
replies
158
views
With DESeq2 "Not full rank" Error with design
DESeq2
DEs
13 days ago • updated 11 days ago
feather-W
• 0
1
vote
3
replies
313
views
DEseq2 coefficient
DESeq2
coefficient
4 weeks ago • updated 12 days ago
JKim
• 0
4
votes
4
replies
1.0k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2
Dese
DifferentialRegulation
differe
updated 13 days ago by
feather-W
• 0 • written 11 months ago by
Bernardo
▴ 10
0
votes
4
replies
350
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 13 days ago by
Michael Love
41k • written 14 days ago by
Jad
• 0
0
votes
2
replies
156
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
14 days ago • updated 13 days ago
kcarey
• 0
0
votes
2
replies
244
views
Missing Band on Volcano Plot from DESeq2
DESeq2
Visualization
DifferentialExpression
updated 13 days ago by
Michael Love
41k • written 15 days ago by
gglatzer
• 0
1
vote
1
reply
165
views
i'm not getting any differentially expressed genes.
DESeq2
updated 15 days ago by
ATpoint
★ 4.0k • written 15 days ago by
Marilyn
• 0
2
votes
1
reply
190
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 15 days ago by
ATpoint
★ 4.0k • written 15 days ago by
hemantcnaik
• 0
6
votes
11
replies
3.7k
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
updated 16 days ago by
Priya
• 0 • written 3.1 years ago by
Marina
▴ 40
1
vote
1
reply
160
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 17 days ago by
ATpoint
★ 4.0k • written 17 days ago by
synat.keam
• 0
0
votes
3
replies
306
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 7 weeks ago by
pl23
• 0
0
votes
2
replies
272
views
DESeq2: Comparing A Knockout to a Strain
DESeq2
20 days ago • updated 18 days ago
Viktor Thiel
• 0
0
votes
1
reply
136
views
DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2
scCITE-seq
updated 20 days ago by
ATpoint
★ 4.0k • written 20 days ago by
daiane.hemerichbrennan
• 0
0
votes
8
replies
293
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
21 days ago • updated 20 days ago
michelafrancesconi8
• 0
0
votes
2
replies
1.4k
views
DE genes over time with DESeq2
deseq2
timecourse
design and contrast matrix
updated 20 days ago by
ta_awwad
▴ 10 • written 8.4 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
150
views
Unusually large fold-changes in Deseq2 results
DESeq2
updated 21 days ago by
ATpoint
★ 4.0k • written 21 days ago by
Sneha
• 0
1
vote
4
replies
233
views
DESeq2 Replicates
DESeq2
RNASeq
21 days ago
kcarey
• 0
2
votes
6
replies
262
views
Factor vs Character in design
DESeq2
21 days ago
James Aiden
• 0
1
vote
3
replies
245
views
Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2
glmGamPoi
27 days ago • updated 21 days ago
I-Hsuan Lin
▴ 10
4
votes
7
replies
754
views
weird volcano plot
DESeq2
updated 22 days ago by
Shuning
• 0 • written 4 months ago by
shouzheng
▴ 10
0
votes
1
reply
219
views
DEseq2 dispersion plot
DESeq2
updated 22 days ago by
Michael Love
41k • written 27 days ago by
Emma
• 0
1
vote
3
replies
256
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 23 days ago by
swbarnes2
★ 1.3k • written 26 days ago by
sap275
▴ 10
0
votes
3
replies
225
views
Would I treat surrogate variables as batches?
DESeq2
sva
updated 23 days ago by
James W. MacDonald
65k • written 27 days ago by
MEME
▴ 10
3
votes
5
replies
541
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 23 days ago by
Michael Love
41k • written 4 weeks ago by
sap275
▴ 10
0
votes
2
replies
293
views
Is DESeq2 normalisation appropriate when counts were obtained for a small number of genes?
DESeq2
updated 25 days ago by
ATpoint
★ 4.0k • written 27 days ago by
Suvi
• 0
1
vote
4
replies
264
views
Further clarification of unbalanced group sizes DESeq2
DESeq2
27 days ago • updated 26 days ago
hmillike
• 0
0
votes
1
reply
190
views
Changed DESeq2 comparison value but the heatmap is still the same
DESeq2
pheatmap
updated 27 days ago by
James W. MacDonald
65k • written 27 days ago by
zhangaimei
• 0
0
votes
13
replies
575
views
Unexpected behavior of lfcShrink() function in DESeq2 analysis
DESeq2
SmallRNA
updated 28 days ago by
Michael Love
41k • written 4 weeks ago by
r.r.bioinf
• 0
0
votes
2
replies
397
views
help checking the design matrix and contrast in DESeq2 "not full rank" scenario
DESeq2
6 weeks ago • updated 28 days ago
ccshao
▴ 70
0
votes
1
reply
143
views
few significant genes from DESeq2 analysis
DESeq2
updated 28 days ago by
Michael Love
41k • written 29 days ago by
Ming
• 0
1
vote
12
replies
955
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison
DESeq2
InteractionSet
pvalue
5 weeks ago • updated 29 days ago
paria.alipour
• 0
43 results • Page
1 of 1
Recent ...
Replies
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Answer: Merging featureCounts output for different species
by
Michael Love
41k
Bioconductor support site is for posting questions about software. Try biostars.
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
Circumvent creating .ff files in the working directory when using genotype.Illumina() function
Answer: Problem with maplot {affy} method when using rma {affy} method output as its inp
Answer: Microarray Limma Model fitting and DEG
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Hervé Pagès
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