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DESeq2
•
reset
0
votes
0
replies
3
views
Slightly different count plots from R and spreadsheet
DESeq2
ggplot2
6 minutes ago • updated 4 minutes ago
boczniak767
▴ 720
1
vote
3
replies
119
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 1 day ago by
James W. MacDonald
66k • written 2 days ago by
boczniak767
▴ 720
2
votes
4
replies
200
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 1 day ago by
Michael Love
42k • written 4 days ago by
shaunpeterson
• 0
0
votes
6
replies
573
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
5 days ago • updated 1 day ago
Ken C
• 0
4
votes
9
replies
302
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 6 days ago by
ATpoint
★ 4.1k • written 7 days ago by
pangtaihin
• 0
0
votes
3
replies
145
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 7 days ago by
Michael Love
42k • written 7 days ago by
Kasper
• 0
1
vote
2
replies
265
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
8 days ago • updated 5 days ago
BioinfGuru
▴ 30
0
votes
8
replies
543
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 7 days ago by
BioinfGuru
▴ 30 • written 8 days ago by
Eric Katagirya
• 0
0
votes
1
reply
112
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 7 days ago by
Michael Love
42k • written 8 days ago by
piemmea
• 0
0
votes
1
reply
189
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 12 days ago by
ATpoint
★ 4.1k • written 12 days ago by
sajadahmad41454
• 0
0
votes
1
reply
116
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 13 days ago by
ATpoint
★ 4.1k • written 13 days ago by
sajadahmad41454
• 0
2
votes
7
replies
435
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
14 days ago • updated 11 days ago
sajadahmad41454
• 0
2
votes
3
replies
265
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 17 days ago by
ATpoint
★ 4.1k • written 18 days ago by
Reza
• 0
1
vote
1
reply
197
views
Handling multiple differential expression comparisons
DESeq2
updated 17 days ago by
Michael Love
42k • written 18 days ago by
Zainab
▴ 10
0
votes
6
replies
309
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 18 days ago by
swbarnes2
★ 1.4k • written 19 days ago by
arfranco
▴ 130
0
votes
2
replies
176
views
DESeq2 v1.35.0
DESeq2
updated 19 days ago by
Michael Love
42k • written 19 days ago by
Espresso
• 0
0
votes
2
replies
219
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
20 days ago • updated 19 days ago
kcarey
• 0
0
votes
3
replies
233
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 20 days ago by
ATpoint
★ 4.1k • written 20 days ago by
james.zhang20
• 0
1
vote
3
replies
314
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 14 days ago by
ATpoint
★ 4.1k • written 20 days ago by
angelathuynh5
• 0
0
votes
3
replies
308
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 20 days ago by
Michael Love
42k • written 21 days ago by
HAK
• 0
1
vote
1
reply
161
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 21 days ago by
Michael Love
42k • written 22 days ago by
marcusn
• 0
0
votes
1
reply
141
views
putting my own expression data in deseq2
DESeq2
updated 22 days ago by
ATpoint
★ 4.1k • written 22 days ago by
Dev
• 0
0
votes
2
replies
174
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
22 days ago • updated 19 days ago
Aurora
• 0
0
votes
1
reply
142
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 21 days ago by
Michael Love
42k • written 22 days ago by
Agung
• 0
3
votes
3
replies
276
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 23 days ago by
ATpoint
★ 4.1k • written 23 days ago by
bioinf
▴ 10
1
vote
3
replies
259
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 26 days ago by
Michael Love
42k • written 26 days ago by
JalapenoCornbread
• 0
2
votes
9
replies
432
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 26 days ago by
James W. MacDonald
66k • written 27 days ago by
Alexandre
• 0
0
votes
2
replies
230
views
PCA plot suggestions
DESeq2
PCAtools
updated 25 days ago by
Michael Love
42k • written 27 days ago by
Aaliya
• 0
0
votes
1
reply
168
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 27 days ago by
Michael Love
42k • written 27 days ago by
kcarey
• 0
1
vote
3
replies
242
views
Different Shrunk Log2FC according with reference
DESeq2
updated 28 days ago by
Michael Love
42k • written 28 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
363
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
28 days ago • updated 26 days ago
winwater0928
• 0
3
votes
1
reply
331
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 28 days ago by
Michael Love
42k • written 28 days ago by
i.sudbery
▴ 40
0
votes
8
replies
404
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 27 days ago by
swbarnes2
★ 1.4k • written 28 days ago by
Aaliya
• 0
3
votes
3
replies
256
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 28 days ago by
Michael Love
42k • written 29 days ago by
WardDeb
• 0
0
votes
1
reply
160
views
rlog transformation
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
ishij9717
• 0
0
votes
1
reply
132
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
09191919
• 0
0
votes
4
replies
272
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
4 weeks ago
lonn
• 0
1
vote
2
replies
762
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 25 days ago
Patadù
▴ 10
0
votes
1
reply
171
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 4 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
quanah.hudson
• 0
0
votes
1
reply
151
views
covariate with negative and positive values
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 5 weeks ago by
Brynn
• 0
0
votes
3
replies
236
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 5 weeks ago by
Michael Love
42k • written 5 weeks ago by
andrebolerbarros
▴ 20
0
votes
4
replies
295
views
DEG with low counts
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 5 weeks ago by
Rajat
• 0
0
votes
1
reply
153
views
Deseq2 Rlog transformation
DESeq2
updated 5 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
Sahar
• 0
1
vote
2
replies
217
views
Design Matrix within group comparison more than two groups
DESeq2
5 weeks ago
hemantcnaik
• 0
0
votes
1
reply
155
views
Bioinformatics student
Des
DESeq2
updated 5 weeks ago by
hemantcnaik
• 0 • written 5 weeks ago by
Sahar
• 0
0
votes
1
reply
202
views
DESeq2 gives an error and R crashes
DESeq2
5 weeks ago
Shefali
• 0
1
vote
2
replies
268
views
How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 4 weeks ago
Weiqian
▴ 10
0
votes
1
reply
196
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 6 weeks ago by
Michael Love
42k • written 6 weeks ago by
Adelaide
• 0
0
votes
2
replies
184
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 6 weeks ago by
James W. MacDonald
66k • written 6 weeks ago by
joshua.mannheimer
• 0
0
votes
2
replies
250
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 6 weeks ago by
Michael Love
42k • written 6 weeks ago by
nhaus
▴ 30
50 results • Page
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Recent ...
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Comment: recount3 problem downloading data from source sra
by
PABLO ANTONIO
• 0
Hello Leonardo, Thanks for commenting on possible solutions. I noticed comparing your session info that I was using the previous version o…
Comment: seqlevelsStyle() not working
by
websterdelacruz2087055
• 0
Specify the new URL new_url <- "https://hgdownload2.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz" Use the new URL to download th…
Comment: SGSeq: moving toward diffex from SGSeq analysis
by
Sara
• 0
Yes, thank you. I have another error now, may you please guide me. here is the code that I used till using vep: ```r # bam_path <- "~/pat…
Comment: slingshot: error with plot3d.SlingshotDataSet
by
Happiness
• 0
Hi please i am encountering similar issue how did you fix it. Here is the code: ## Run Slingshot p3.neuron.sds <- slingshot(Embeddings(…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
by
mohammedtoufiq91
▴ 10
https://support.bioconductor.org/u/5106/ thank you very much.
Votes
Answer: Multiple factor DSEq2 result generates weird volcano plot
DESeq2 for single cell pseudobulk processing
Simultaneously adding two different covariates in the model gives error in DESeq2.
How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: recount3 problem downloading data from source sra
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