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DESEQ2
•
reset
0
votes
2
replies
2.2k
views
error in file(file, "rt") when reading in sample sheet using DESeqDataSetFromHTSeqCount
DESeq2
4.4 years ago
Yihan
• 0
1
vote
2
replies
1.0k
views
Doing multiple comparisons in a DESeq2 object with multiple conditions
DESeq2
4.4 years ago • updated 4.3 years ago
jenabris
• 0
3
votes
16
replies
3.8k
views
DESeq2 - groups with biological replicates from the same patient
DESeq2
updated 22 months ago by
shepherl
4.2k • written 4.4 years ago by
S
▴ 10
0
votes
4
replies
2.8k
views
estimateSizeFactors throws "Error in .local(object, ..., value) : all(!is.na(value)) is not TRUE". Identified root cause within estimateSizeFactorsFo…
DESeq2
4.4 years ago
alawrence2211
• 0
3
votes
4
replies
4.7k
views
Clarification re VST transformed data in DESeq2
DESeq2
updated 4.4 years ago by
ATpoint
★ 5.0k • written 4.4 years ago by
Nikolay Ivanov
• 0
0
votes
1
reply
1.4k
views
DESseq2 question about VST and rlog
DESeq2
Normalization
updated 4.4 years ago by
ATpoint
★ 5.0k • written 4.4 years ago by
Golden-proteogenomics
• 0
2
votes
1
reply
989
views
estimateSizeFactors before or after removing non-coding genes and filtering for low counts
DESeq2
RNASeq
updated 4.4 years ago by
Michael Love
43k • written 4.4 years ago by
Tash.
• 0
3
votes
3
replies
1.8k
views
How is DESeq2 handling replicates?
DESeq2
updated 4.4 years ago by
Michael Love
43k • written 4.4 years ago by
XTR5
▴ 10
0
votes
6
replies
1.5k
views
Bias of lowly expressed genes in DESeq2
DESeq2
updated 4.4 years ago by
Michael Love
43k • written 4.4 years ago by
Jason
• 0
0
votes
2
replies
2.5k
views
DESeq2 for longitudinal data
DESeq2
updated 4.4 years ago by
Michael Love
43k • written 4.4 years ago by
lovelymaoqin
• 0
0
votes
3
replies
942
views
Highly left- skewed raw pvalues from DESeq2 analysis
DESeq2
updated 4.4 years ago by
Michael Love
43k • written 4.4 years ago by
tornadow18
• 0
0
votes
6
replies
1.3k
views
DESeq2 time course confusion
DESeq2
DifferentialExpression
4.4 years ago
rajpal22288
▴ 10
2
votes
2
replies
884
views
dispersion increasing for extreme high mean counts
DESeq2
4.4 years ago
XTR5
▴ 10
0
votes
2
replies
1.9k
views
Install older version of DESeq2 for use on cluster with older version of R
DESeq2
BiocVersion
updated 4.4 years ago by
glennmaxwell229
• 0 • written 4.4 years ago by
Daisy
• 0
1
vote
5
replies
2.6k
views
how to plot multiple RLEs on same plot?
plotRLE
Nanostring
RUVSeq
DESEQ2
updated 15 months ago by
BioinfGuru
▴ 70 • written 4.4 years ago by
xiaofeiwang18266
▴ 60
1
vote
1
reply
1.4k
views
DESeq2 for allele-specific expression with contrasts between conditions
DESeq2
AllelicImbalance
edgeR
RNASeq
updated 4.4 years ago by
Michael Love
43k • written 4.4 years ago by
Katya
• 0
1
vote
3
replies
1.4k
views
DESeq2: NA's in mcols(object)$betaConv
DESeq2
updated 4.4 years ago by
Michael Love
43k • written 4.4 years ago by
Nikolay Ivanov
• 0
0
votes
2
replies
725
views
DESeq2: One or more designs for contrasts of interest
DESeq2
4.4 years ago
Mirin1357
• 0
2
votes
2
replies
2.4k
views
DESeq2 - one groups with no replicates
DESeq2
rnaseqGene
DifferentialExpression
GeneExpression
4.4 years ago
SUMIT
• 0
0
votes
2
replies
2.4k
views
PCA and heatmaps: most variable genes selection
DESeq2
ExpressionData
heatmaps
pca
4.4 years ago
Clara
▴ 10
2
votes
6
replies
6.1k
views
Salmon, RUVSeq and DESeq2
Salmon
DESeq2
DEG
RUVSeq
4.4 years ago
reganhayward
• 0
3
votes
5
replies
4.3k
views
Negative binomial fitting DESeq2
DESeq2
RNA-seq
updated 4.4 years ago by
Michael Love
43k • written 4.4 years ago by
Lucy
▴ 60
0
votes
7
replies
1.5k
views
matrix with Salmon gene-level quantifications in DESeq
DESeq2
4.4 years ago
luca.s
▴ 50
0
votes
8
replies
2.9k
views
DESeq2: Variable Importance
DESeq2
RNASeq
updated 4.4 years ago by
Michael Love
43k • written 4.4 years ago by
lolol
• 0
0
votes
1
reply
760
views
DESeq2 - how to account for patient, batch and condition
DESeq2
updated 4.4 years ago by
James W. MacDonald
68k • written 4.4 years ago by
S
▴ 10
2
votes
4
replies
1.7k
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2
RNASeq
BatchEffect
limma
updated 2.2 years ago by
Michael Love
43k • written 4.5 years ago by
athiebaut
• 0
0
votes
9
replies
2.6k
views
Why is my plot count does not fit with log fold change result?
DESeq2
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
Gian
▴ 30
0
votes
4
replies
1.1k
views
Number of genes differs between two design formulas in deseq2
DESeq2
4.5 years ago
Mohamed Malek
• 0
1
vote
6
replies
2.6k
views
Statistics on normalized counts
DESeq2
updated 4.5 years ago by
Rachel
• 0 • written 4.5 years ago by
Justin
• 0
0
votes
3
replies
1.9k
views
[DEseq2] How to properly add a noise coefficient to the experiment design formula
limma
edgeR
DEseq2
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
drowsygoat
▴ 30
1
vote
1
reply
1.0k
views
DESeq2 - DGE in organoids for multiple group comparisons
personalome
organoids
DGE
DESeq2
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
S
▴ 10
0
votes
1
reply
725
views
Why is the number of DEG different when comparing A versus B and B versus A?
DESeq2
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
ชัยวัฒน์
• 0
0
votes
2
replies
1.4k
views
where to download practice data
DESeq2
updated 4.5 years ago by
ATpoint
★ 5.0k • written 4.5 years ago by
jinliqin
• 0
0
votes
1
reply
975
views
DESeq2: Paired samples (before and after treatment) with different responses
DESeq2
updated 4.5 years ago by
swbarnes2
★ 1.4k • written 4.5 years ago by
allopathie
• 0
2
votes
2
replies
905
views
How to remove batch effect from multiple rna-seq dataset before running deseq2
DESeq2
4.5 years ago
Yosapol
• 0
0
votes
1
reply
1.6k
views
Creating a DESeqDataSet from a RangedSummarizedExperiment - where is the design parameter in RangedSummarizedExperiment
SRA
DESeq2
4.5 years ago
Serge
• 0
0
votes
3
replies
1.4k
views
Contrasting LogFCs in DESeq2
DESeq2
RNASeqData
updated 4.5 years ago by
swbarnes2
★ 1.4k • written 4.5 years ago by
GlycineMax
• 0
1
vote
1
reply
1.7k
views
[DESeq2] - Making DESeq Dataset object from csv of already normalized counts.
DESeq2
4.5 years ago
Michael
• 0
0
votes
2
replies
802
views
DESeq2 - Cannot replicate log2FC calculations
DESeq2
4.5 years ago
Sara
• 0
2
votes
2
replies
2.2k
views
DESeq2 time-series with two conditions and several patients
DESeq2
4.5 years ago • updated 4.4 years ago
Karolina Trachtova
▴ 10
1
vote
2
replies
2.2k
views
Design Formula, PCA, and Sex Effect
DESeq2
4.5 years ago
GHI
▴ 10
0
votes
5
replies
1.8k
views
Tximport/DESeq2 Normalization Process
tximport
Normalization
DESeq2
updated 4.4 years ago by
Michael Love
43k • written 4.5 years ago by
johnsony
• 0
4
votes
3
replies
2.1k
views
Concatenating expression counts from different RNA-seq quantification tools
tximport
HERVs
edgeR
DESeq2
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
rodrigo.duarte88
▴ 40
0
votes
1
reply
1.2k
views
FDR Correction
dada2
Metagenomics
DESeq2
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
GlycineMax
• 0
2
votes
8
replies
3.0k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression
DESeq2
contrasts
4.5 years ago
Jane
▴ 10
6
votes
12
replies
3.1k
views
ColData use only certain variable within
DESeq2
4.5 years ago
Bine
▴ 50
0
votes
2
replies
2.0k
views
Error in DESeqDataSetFromMatrix()
DESeq2
RNAseq
updated 3.4 years ago by
Luke
▴ 10 • written 4.5 years ago by
elizabethe819
• 0
1
vote
2
replies
3.5k
views
Plotting FPKM
ggplots2
DESeq2
fpkm()
4.5 years ago
GA
▴ 10
1
vote
4
replies
1.1k
views
Incorrect 2-fold change reported in DESeq2 Data
DESeq2
4.5 years ago
Naphtap92
▴ 10
0
votes
3
replies
2.0k
views
Can't install DESeq2 because of libxml
deseq2
libxml
xml
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
Fátima
• 0
4,839 results • Page
29 of 97
Recent ...
Replies
Comment: Post translational modifications and phosphoproteomics in limpa?
by
james.eapen
• 0
Thank you!
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
ATpoint
★ 5.0k
The donor effect is crystal clear, and absent in these suspicious samples. It strongly argues for a technical problem. If you really need s…
Answer: mzR-Rcpp compiler version issue
by
Laurent Gatto
1.6k
There are two issues here. First, a warning about mzR, that you can safely ignore. It tells you that mzR was compiled using a different …
Comment: Identifying differentially expressed genes in individual samples from a large co
by
jamie.gearing
▴ 60
Great. Yes, something descriptive is probably good enough, even if the p-values themselves are not so rigorous. Thanks very much Gordon!
Comment: Co-occurrence Network Analysis between Algae and Bacteria
by
Stefano Mangiola
▴ 40
Just a placeholder, that we are extending `sccomp` to co-occurrence analyses. Yours could be a good use-case to test first. We will be in t…
Votes
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
Answer: Identifying differentially expressed genes in individual samples from a large co
Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
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