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DESEQ2
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0
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4
replies
2.3k
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How to analyze RNAseq data with multiple treatment groups and each subject has pre and post-treatment measures using deseq2/edger/limma?
deseq2
limma
edger
Tutorial
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
wwu222
• 0
0
votes
1
reply
945
views
Independent dataset comparison, design definition and average of contrasts in Deseq2
Deseq2
design definition
average of contrasts
singe-cell
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
baldissera152
• 0
0
votes
2
replies
768
views
Find the expected counts in DESeq2 output
deseq2
updated 6.7 years ago by
swbarnes2
★ 1.4k • written 6.7 years ago by
cwliu2014
• 0
3
votes
2
replies
1.2k
views
model matrix design for DESeq2 for use with lfcShrink function
deseq2
model.matrix
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
toddknutson
• 0
3
votes
5
replies
1.2k
views
Accounting for batch effect in DESseq2
deseq2
batch_effect
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
gtechbio
▴ 10
1
vote
1
reply
1.2k
views
Finding genes that are expressed only in one condition within a contrast
filter
deseq2
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
charles.foster
▴ 180
0
votes
1
reply
878
views
Multiple comparisons with Deseq2
deseq2
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
gilles.charpigny
• 0
1
vote
1
reply
4.2k
views
DESeq2 coldata and count data subset
deseq2
differential gene expresssion
updated 6.7 years ago by
Martin Morgan
25k • written 6.7 years ago by
lalchungnungabt17
• 0
0
votes
1
reply
658
views
randomized design (Treatment and time)
deseq2
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
JP
• 0
0
votes
3
replies
1.1k
views
DEseq2: Why low counts mean count < 804
deseq2
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
lihongfei93
• 0
1
vote
2
replies
869
views
Design definition with multiple conditions in DESeqDataSetFromMatrix
deseq2
6.7 years ago
silvia.morini01
• 0
2
votes
6
replies
2.6k
views
Normalisation for count data visualisation only
deseq2
salmon
tximport
normalization
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
Alex So
• 0
0
votes
1
reply
1.0k
views
DESeq2 : Calculation of rlog (regularized log transformation)
deseq2
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
surabhijagtap95
• 0
0
votes
8
replies
4.8k
views
DESEQ2 - help with interpreting time series heatmaps and resultsName
deseq2
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
courtney.stairs
• 0
0
votes
1
reply
717
views
Contrast argument in DEseq
deseq2
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
hamsasekar02
• 0
0
votes
15
replies
3.6k
views
Phyloseq to deseq2
deseq2
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
Jitendra
▴ 10
1
vote
3
replies
1.4k
views
Design matrix: DESeq2
deseq2
6.7 years ago
Gyan Prakash Mishra
▴ 10
0
votes
1
reply
731
views
Interaction term for condition, time point and genotypes together in DESeq2
deseq2
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
hamsasekar02
• 0
0
votes
2
replies
962
views
Usage of interactions for multi-factor analysis
deseq2
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
lihongfei93
• 0
0
votes
2
replies
1.3k
views
DESEQ2: rnaseqGene fisison tutorial time course graph has non-numerical x-axis
deseq2
rnaseqGene
6.7 years ago
courtney.stairs
• 0
0
votes
2
replies
1.2k
views
Indentify DESeq2 is take too long
deseq2
6.7 years ago
lucianalpt
• 0
0
votes
6
replies
1.8k
views
How do I prevent my R kernel (Jupyter Notebook) from dying after running variance stabilizing transformation?
deseq2
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
david.wheeler7
▴ 20
5
votes
5
replies
8.2k
views
Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2
scRNA-Seq
RNA-Seq
differential expression analysis
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
hamza_karakurt
▴ 60
3
votes
9
replies
6.3k
views
txi <- tximport(files, type="salmon", tx2gene=tx2gene) Error in tximport(files, type = "salmon", tx2gene = tx2gene) : all(file.exists(files)) is n…
deseq2
tximport
file.path
files
file.exists
6.7 years ago
Leo K
• 0
0
votes
6
replies
2.5k
views
DESeq2; loading htseq-count output; sample condition is described in a different csv file
deseq2
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
mzillur
• 0
1
vote
2
replies
2.5k
views
DeSEQ2- What is the difference between Gene Clustering and using LRT for Time Series experiment WITHOUT treatments
deseq2
Time Series
Gene Clustering
LRT
ATACseq
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
kaiser.karim
• 0
1
vote
1
reply
1000
views
Significance of the interaction term in DESeq2
deseq2
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
cihan.erkut
▴ 10
0
votes
4
replies
1.2k
views
What will lead DESeq2 shows no DEGs if workflow adopted is okay?
deseq2
updated 6.7 years ago by
arfranco
▴ 130 • written 6.7 years ago by
gmumuxi
• 0
0
votes
1
reply
935
views
Getting a signature specific to each patient
DESeq2
r
cancer
updated 6.7 years ago by
James W. MacDonald
68k • written 6.7 years ago by
AZ
▴ 30
1
vote
5
replies
2.4k
views
Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2
DE
DEG
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
hermanapis
• 0
0
votes
7
replies
2.1k
views
Problems with DESeq2 'design' parameter using Shiny/rhandsontable
deseq2
shiny
design
rhandsontable
hot_to_r()
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
hinkel2
• 0
1
vote
2
replies
673
views
DESeq2: Errors in .Call(.NAME, ..., PACKAGE = PACKAGE)
DESeq2
Errors
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
joy@wh
• 0
1
vote
1
reply
759
views
Bringing in data for DESeq2, can't match first column colData to column names of countData
deseq2
bioconductor
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
ishtarredman
• 0
0
votes
5
replies
3.0k
views
Getting opposite log2 fold change
deseq2
gene expression
log2foldchange
R
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
leekun4
• 0
0
votes
2
replies
1.9k
views
Very high threshold for independent filtering
deseq2
mirna
independent filtering
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
thomas.deimel
• 0
3
votes
7
replies
30k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2
gsea
rnaseq
gene espression
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
bmreilly
• 0
0
votes
2
replies
1.1k
views
Adjusting DESeq2 p-values through IHW using pathway information as covariate
IHW
deseq2
Pathway
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
guidobarzaghi
▴ 20
2
votes
2
replies
2.3k
views
How to extract factor levels of coldata from deseq object?
deseq2
levels
factor
colData
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
ariel
▴ 20
0
votes
5
replies
1.1k
views
Batch correction with DeSeq2: problem with creating model and getting all conditions
deseq2
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
pkhadka
• 0
2
votes
4
replies
5.0k
views
How to reconfigure Jupyter Notebook to locate specific version of R?
deseq2
software error
6.7 years ago
david.wheeler7
▴ 20
0
votes
4
replies
1.0k
views
DESeq2: Second order interactions
deseq2
updated 6.7 years ago by
Michael Love
43k • written 6.8 years ago by
Pindre
• 0
0
votes
1
reply
1.3k
views
Using STAR and DESeq2 for circRNA analysis
STAR
deseq2
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
csijst
• 0
4
votes
10
replies
7.5k
views
Random Effect in DESeq2
deseq2
updated 4.0 years ago by
galen.seilis
• 0 • written 6.8 years ago by
susana.amaral.teixeira
▴ 20
1
vote
1
reply
1.9k
views
News:
Bioinformatics Summer School - July 2019 - UCLouvain (Belgium)
RNAseq
deseq2
proteomics
transcriptomics
workshop
News
written 6.7 years ago by
Laurent Gatto
1.6k
4
votes
6
replies
4.6k
views
DESeq2 vst normalization: Do I have a heteroscedasticity problem and if so, what can I do about it?
deseq2
normalization
rna-seq
TCGA
vst
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
Marc Saric
▴ 70
1
vote
26
replies
8.5k
views
How can I install DeSeq2 in Jupyter Notebook?
deseq2
updated 6.7 years ago by
Marc Saric
▴ 70 • written 6.8 years ago by
david.wheeler7
▴ 20
0
votes
1
reply
729
views
Is it required to specify Outliers function in DESeq2
deseq2
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
angajalaanusha
▴ 10
0
votes
2
replies
1.5k
views
Different results in DESeq2 when using betaPrior=TRUE and betaPrior=FALSE
deseq2
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
sven.schenk
▴ 30
0
votes
9
replies
2.9k
views
NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq
deseq2
contrast
subgroup
6.8 years ago
ariel
▴ 20
0
votes
1
reply
914
views
DESeq2 Multiple Comparison Testing with Contrasts
deseq2
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
jonathan.diedrich
• 0
4,839 results • Page
53 of 97
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