Showing : DESeq2 • reset
17
votes
45
replies
13k
views
Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 3 months ago by 68k • written 6.4 years ago by ▴ 60
5
votes
30
replies
6.7k
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 8 months ago by • 0 • written 8.5 years ago by ▴ 10
34
votes
29
replies
17k
views
[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 15 months ago by 43k • written 10.8 years ago by ▴ 130
1
vote
26
replies
8.7k
views
How can I install DeSeq2 in Jupyter Notebook?
deseq2
updated 6.8 years ago by ▴ 70 • written 6.8 years ago by ▴ 20
31
votes
25
replies
62k
views
deseq2 filter the low counts
deseq2 lowcount
updated 6 weeks ago by 43k • written 10.8 years ago by ▴ 40
0
votes
25
replies
4.1k
views
deseq2 course experiment
deseq2
8.6 years ago • updated 8.5 years ago ribioinfo ▴ 100
10
votes
23
replies
16k
views
Macbook M1 install genefilter failed
DESeq2 m1 macbook genefilter
4.4 years ago • updated 3.1 years ago soda ▴ 80
2
votes
23
replies
5.2k
views
Coping with a label/class imbalance in DESeq2
deseq2 rnaseq r regression
updated 9.2 years ago by 43k • written 9.2 years ago by • 0
38
votes
23
replies
18k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
11.3 years ago • updated 9 months ago Michael Love 43k
14
votes
22
replies
34k
views
DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 22 months ago by 43k • written 9.5 years ago by ▴ 30
1
vote
22
replies
6.4k
views
DESEq2 Large Memory When Parallel
deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 10
27
votes
22
replies
23k
views
DESeq2 for ChIP-seq differential peaks
deseq2 deseq chipseq
updated 8.5 years ago by ▴ 120 • written 10.3 years ago by ▴ 200
1
vote
22
replies
6.3k
views
DESeq2 for Ribosomal profiling analysis
deseq2
9.7 years ago jxu006 ▴ 10
4
votes
21
replies
14k
views
DESeq2 and ComBat
deseq2 combat
updated 9.9 years ago by ▴ 610 • written 9.9 years ago by ▴ 100
0
votes
20
replies
3.8k
views
DESeq2 question: why I got discrepancy results for DEGs when using different ways setting up the models
DESeq2 DEGs
4.4 years ago Ming ▴ 380
1
vote
20
replies
6.7k
views
Deseq2 installed, but there is no package called ‘Biostrings’
DESeq2 Install
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
2
votes
20
replies
4.2k
views
plotPCA in DESeq2
software error deseq2
5.5 years ago yueli7 ▴ 20
52
votes
20
replies
52k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 9.5 years ago by • 0 • written 10.0 years ago by ▴ 110
0
votes
20
replies
3.5k
views
Different DESeq2 results (both FC and pvalue) by changing col/row orders in input
DESeq2
3.5 years ago Weisheng • 0
10
votes
20
replies
27k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
updated 14 months ago by 68k • written 6.6 years ago by ▴ 30
0
votes
19
replies
2.8k
views
Paired Difference Analysis
deseq2 R differential gene expression
8.3 years ago • updated 8.2 years ago nhua • 0
14
votes
19
replies
10k
views
DESeq2 Model Design
DESeq2 linear model model
updated 4.6 years ago by 43k • written 11.1 years ago by ▴ 370
6
votes
19
replies
5.2k
views
Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 8.2 years ago by ▴ 690 • written 8.2 years ago by ▴ 50
16
votes
19
replies
22k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
updated 3.9 years ago by ▴ 60 • written 11.1 years ago by ▴ 130
6
votes
19
replies
5.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 19 months ago by • 0 • written 6.2 years ago by ▴ 10
5
votes
19
replies
7.4k
views
lfcShrink and factors with multiple levels
deseq2 lfcshrink relevel
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 110
0
votes
18
replies
3.8k
views
DESeq2 in R_devel: a bug?
DESeq2 DESeq2
updated 11.8 years ago by 43k • written 11.8 years ago by ▴ 80
15
votes
18
replies
5.2k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2 edgeR goana GO
updated 3.7 years ago by 53k • written 3.7 years ago by ▴ 60
0
votes
18
replies
6.0k
views
DEseq2 metagenomic analysis without replicates
DESeq2 DESeq2
updated 11.9 years ago by ▴ 220 • written 11.9 years ago by ★ 13k
1
vote
18
replies
5.6k
views
DESEQ2 linear model of dose
deseq2
updated 9.2 years ago by ★ 3.8k • written 9.2 years ago by ▴ 10
0
votes
18
replies
3.9k
views
DESeq2: Possible issue with colData and sorting
deseq2 summarizedexperiment
updated 9.2 years ago by 25k • written 9.3 years ago by ▴ 40
3
votes
18
replies
4.1k
views
DESeq2 filter out my expression gene
deseq2
updated 9.9 years ago by 43k • written 9.9 years ago by ▴ 40
5
votes
18
replies
9.6k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor Install DESeq2
updated 24 months ago by • 0 • written 3.9 years ago by • 0
8
votes
18
replies
17k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 4.8 years ago by • 0 • written 6.2 years ago by ▴ 10
0
votes
18
replies
4.6k
views
Subset-ing Large DESeqDataSet for data extraction with contrast function
deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
5
votes
18
replies
4.3k
views
DESeq2 comparison two cell types and two genotypes
GeneExpressionWorkflow DESeq2 GeneExpression
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
5
votes
18
replies
2.8k
views
Difference of difference, paired design
edger deseq2 limma
updated 6.4 years ago by ★ 1.4k • written 6.4 years ago by • 0
4
votes
18
replies
27k
views
DEseq2 time-series design.
deseq2 timecourse design
updated 6.5 years ago by • 0 • written 11.1 years ago by ▴ 100
4
votes
18
replies
9.2k
views
DESeq2 - multifactorial design
LRT DESeq2 interaction
updated 4.7 years ago by ★ 4.0k • written 4.8 years ago by ▴ 10
12
votes
18
replies
7.5k
views
What is the correct use of removeBatchEffect's design parameter
deseq2 limma
updated 4.8 years ago by 53k • written 5.3 years ago by ▴ 10
7
votes
17
replies
6.8k
views
DESeqDataSetFromTximport: Error in checkSlotAssignment
deseq2 tximport
8.6 years ago JWCarlson ▴ 80
9
votes
17
replies
2.7k
views
DESeq2 design subcategories
deseq2 deseq differential binding analysis
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 60
2
votes
17
replies
5.3k
views
Multi-factorial design in DEseq2: defining reduced model
deseq2 multifactorial design reduced model
8.9 years ago laianavarromartin ▴ 20
2
votes
17
replies
3.9k
views
Computationally Singular Matrices - DESeq
deseq2 rnaseq sva
updated 3.1 years ago by 43k • written 6.7 years ago by • 0
0
votes
17
replies
10k
views
DESeq2 Error NA values
deseq2
updated 10.5 years ago by 43k • written 10.5 years ago by ▴ 60
2
votes
17
replies
3.3k
views
How to reduce the impact of one varaible in Deseq2 or edgeR for multivariate value analysis?
MultipleComparison edgeR DESeq2
written 3.7 years ago by • 0
0
votes
17
replies
4.9k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 2.5 years ago by • 0 • written 8.2 years ago by • 0
27
votes
17
replies
10.0k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 4.6 years ago by 43k • written 7.5 years ago by ▴ 50
0
votes
17
replies
3.9k
views
DESeq2 shrunken log fold changes
deseq2
5.7 years ago dequattro.concetta ▴ 10
2
votes
17
replies
4.2k
views
DESeq2- what to do when two conditions share controls?
deseq2
8.6 years ago grashow ▴ 10
4,841 results • Page 1 of 97
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Replies
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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