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Showing :
DESeq2
•
reset
0
votes
10
replies
1.9k
views
DESeq2 filtering vs edgeR filtering
DESeq2
written 23 months ago by
fr8712ca-s
• 0
5
votes
11
replies
4.0k
views
parameters of filterByExpr
edgeR
DESeq2
filterByExpr
written 9 months ago by
caroline.zanchi
▴ 10
3
votes
13
replies
2.4k
views
Highly DE genes but small count difference within conditions
RNASeq
DESeq2
RNASeqData
written 16 months ago by
bioshot.com
• 0
17
votes
45
replies
13k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 5 months ago by
James W. MacDonald
68k • written 6.5 years ago by
lim6432
▴ 60
1
vote
3
replies
6.3k
views
DESeq2 estimateSizeFactors with control genes
deseq2
differential gene expression
controls
references
updated 10 months ago by
sofia.rigou
• 0 • written 7.2 years ago by
cris.kgs
• 0
3
votes
2
replies
1.6k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2
RNASeqData
RNASeq
written 8 months ago by
Christian
▴ 20
0
votes
3
replies
414
views
DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva
lfcshrink
DESeq2
7 weeks ago • updated 26 days ago
ja569116
• 0
3
votes
14
replies
1.5k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave
DESeq2
written 6 months ago by
Aurélie
• 0
1
vote
5
replies
4.8k
views
DESeq2 swap ensembl gene id rownames with gene symbol column
deseq2
dataframe
ensembl gene id
gene symbol
entrezid
updated 11 months ago by
Erika
• 0 • written 6.2 years ago by
jason.williams
▴ 10
4
votes
6
replies
1.7k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2
DEXSeq
updated 10 months ago by
ATpoint
★ 5.0k • written 11 months ago by
Elijah
• 0
0
votes
5
replies
2.3k
views
DESeq2 contrast cleaning problem
software error
bugs
deseq2
written 10.0 years ago by
john.hu
• 0
6
votes
4
replies
8.3k
views
DESeq2 with proteomics data
deseq2
updated 9 months ago by
wook2014
• 0 • written 7.6 years ago by
shyu
▴ 10
0
votes
13
replies
844
views
Making a Full Rank Model for Allele-Specific Expression with DESeq2
DESeq2
updated 16 days ago by
Gordon Smyth
53k • written 22 days ago by
chp265
• 0
3
votes
6
replies
1.1k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq
DESeq2
DifferentialExpression
RNASeqData
written 11 weeks ago by
Ahmed Salah
• 0
1
vote
2
replies
2.8k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 8 months ago by
corranna98
• 0
9
votes
3
replies
3.4k
views
DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 8 months ago by
Michael Love
43k • written 9 months ago by
Cassia
▴ 40
31
votes
25
replies
64k
views
deseq2 filter the low counts
deseq2
lowcount
updated 3 months ago by
Michael Love
43k • written 11.0 years ago by
aristotele_m
▴ 40
0
votes
6
replies
648
views
BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel
DESeq2
updated 23 days ago by
Martin Morgan
25k • written 9 weeks ago by
Benjamin
• 0
0
votes
2
replies
208
views
lfc shrinkage estimator in DESeq2
DESeq2
written 16 days ago by
julia_mcdonough
• 0
1
vote
4
replies
184
views
Bulk RNAseq analysis for
DESeq2
RNASeq
edgeR
limma
2 days ago • updated 1 day ago
Mariami
• 0
8
votes
10
replies
18k
views
GSEA preranked analysis downstream of DEseq2
deseq2
gsea
rnaseq
updated 9 months ago by
ATpoint
★ 5.0k • written 9.5 years ago by
EJ
▴ 20
2
votes
4
replies
2.0k
views
Filtering after DESeq
DESeq2
IHW
written 9 months ago by
caroline.zanchi
▴ 10
9
votes
15
replies
7.5k
views
DESeq2 on NanoString Data
deseq2
nanostring
updated 5 months ago by
Michael Love
43k • written 7.7 years ago by
casey.rimland
▴ 170
5
votes
30
replies
6.9k
views
DESeq2 model - How to test case/control time course model when taking account within sample variability?
deseq2
multiple time points
time course
casecontrol
model design
updated 10 months ago by
wuwenhui2
• 0 • written 8.6 years ago by
heikki.sarin
▴ 10
3
votes
1
reply
3.9k
views
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 8 months ago by
Michael Love
43k • written 8 months ago by
Chenghao
▴ 10
0
votes
2
replies
964
views
Analyzing TnSeq data with DESeq2
DESeq2
written 9 months ago by
newfunland
• 0
0
votes
1
reply
680
views
DESeq2 results
result
DESeq2
subsetting
updated 8 months ago by
ATpoint
★ 5.0k • written 8 months ago by
rajdeepboral00
• 0
0
votes
3
replies
1.1k
views
Log2foldchange strange behavior
DESeq2
updated 10 months ago by
ATpoint
★ 5.0k • written 10 months ago by
RambakKulit
• 0
0
votes
6
replies
2.3k
views
DESeq2 It is correct to use interaction term for patient variability?
deseq2
design
interaction term
R
written 8.0 years ago by
briverog
• 0
2
votes
6
replies
2.8k
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 11 months ago by
Jane
• 0 • written 21 months ago by
Reza
• 0
2
votes
2
replies
952
views
Plot title for PCA in DESeq2
DESeq2
11 months ago
AL
• 0
1
vote
2
replies
1.5k
views
Weird p-values using DESeq2?
DESeq2
RNASeq
updated 12 months ago by
ATpoint
★ 5.0k • written 12 months ago by
ingrid.h
• 0
1
vote
6
replies
2.2k
views
how to analysis htseq-count
deseq2
written 8.1 years ago by
Bioinformatics
▴ 30
12
votes
7
replies
23k
views
DESEq2 comparison with mulitple cell types under 2 conditions
deseq2
multiple factor design
updated 9 months ago by
boczniak767
▴ 740 • written 10.8 years ago by
kmu004
▴ 50
0
votes
2
replies
803
views
Design formula for circadian time-course data for vst() function
DESeq2
9 months ago
Vishnu
• 0
1
vote
4
replies
2.9k
views
Pairwise comparison of multiple groups with different base
deseq2
rna-seq
r
updated 24 days ago by
ja569116
• 0 • written 5.7 years ago by
thjnant
▴ 10
5
votes
5
replies
4.1k
views
Cannot extract size factor from DESeq2 analysis
deseq2
tximport
updated 8 months ago by
Michael Love
43k • written 5.8 years ago by
zroger499
• 0
1
vote
5
replies
2.1k
views
p-value the same for different contrasts DESeq2
deseq2
design and contrast matrix
updated 12 months ago by
caroline.zanchi
▴ 10 • written 7.8 years ago by
chitsazanalex
▴ 10
0
votes
3
replies
364
views
DESeq2 inconsistent fits depending on model design with interacting factors
des
DESeq2
written 6 months ago by
fedor.bezrukov
▴ 10
2
votes
5
replies
1.5k
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
11 months ago
picasa1983
• 0
0
votes
3
replies
1.5k
views
PCA subset of genes vs DE
DESeq2
RNASeq
written 3.0 years ago by
andrebolerbarros
▴ 20
1
vote
10
replies
11k
views
DESeq2: Continuous and discreate variables in the design
deseq2
R
rna-seq
design
updated 6 months ago by
Michael Love
43k • written 6.2 years ago by
raquelgarza95
• 0
2
votes
6
replies
693
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
6 months ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
11
replies
823
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse
DESeq2
5 months ago
Denise
• 0
0
votes
5
replies
2.6k
views
DeSeq Strategies for run to run Replication
DESeq2
Normalization
Clustering
replicate
updated 8 months ago by
Michael Love
43k • written 3.5 years ago by
Giorgio
• 0
1
vote
11
replies
2.3k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2
scRNAseq
updated 11 weeks ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
Raya
• 0
4
votes
4
replies
2.2k
views
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2
ComplexHeatmap
8 months ago
caroline.zanchi
▴ 10
0
votes
2
replies
786
views
Differing results with DESeq2
DESeq2
updated 9 months ago by
JKim
• 0 • written 10 months ago by
hampsdiv
• 0
0
votes
2
replies
415
views
DESeq2 on non-RNASeq counts data
DESeq2
written 5 months ago by
vs
• 0
1
vote
3
replies
6.6k
views
Log2 fold change value in DESeq2
deseq2
rnaseq
written 8.3 years ago by
AP
• 0
121 results • Page
1 of 3
Recent ...
Replies
Comment: Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
by
a2a2ddrhaa
• 0
For those taking a break from the lab, the CT777 Game download https://ct7777.pk/ offers a high-performance entry into online mobile gaming…
Answer: Subsetting data verses contrasts [DESeq2]?
by
ATpoint
★ 5.0k
This has been asked many times before, please search for relevant posts. In short: Generally it is least tedious to not split the data and …
Comment: Bulk RNAseq analysis for
by
Mariami
• 0
Thank you so much for your help! will try to proceed with the suggestion
Comment: Bulk RNAseq analysis for
by
Mariami
• 0
Thank you for the explanation. I understand, although at the moment we are limited in our ability to increase N. My concern came from the o…
Answer: Bulk RNAseq analysis for
by
Gordon Smyth
53k
All three packages allow paired comparisons, where the clone is the "pair". limma moreover allows mixed models (just run `voomLmFit` with `…
Votes
Comment: Are transformed values from rlog /vst log2 normalized counts?
Are transformed values from rlog /vst log2 normalized counts?
Answer: Bulk RNAseq analysis for
Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
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