Showing : DESeq2 • reset
12
votes
12
replies
43k
views
[DESEQ2] How to access the normalized data of a DESeqDataSet
deseq2
updated 6.3 years ago by 13k • written 6.4 years ago by ▴ 100
8
votes
10
replies
33k
views
DESeq2 output explanation
deseq deseq2
updated 6.7 years ago by 33k • written 6.7 years ago by ▴ 60
44
votes
20
replies
26k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 5.2 years ago by • 0 • written 5.6 years ago by ▴ 100
21
votes
14
replies
26k
views
deseq2 filter the low counts
deseq2 lowcount
updated 5 months ago by 33k • written 6.4 years ago by ▴ 30
8
votes
4
replies
24k
views
DESeq2 baseMean counts
deseq2
updated 5.7 years ago by 33k • written 5.7 years ago by • 0
13
votes
4
replies
22k
views
FDR and padj in deseq and edger
deseq2 edger
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 60
6
votes
5
replies
20k
views
plotPCA - how to add labels to a PCA plot
plotPCA deseq2 labels
updated 4.6 years ago by ▴ 110 • written 4.6 years ago by ▴ 20
8
votes
10
replies
19k
views
Design formula and Design matrix in DESeq
rnaseq deseq2 formula Limma
6.2 years ago AurelieMLB ▴ 50
13
votes
3
replies
18k
views
DESeq2: Is it possible to convert read counts to expression values via TPM and return these values?
deseq2 r
updated 4.5 years ago by 33k • written 4.5 years ago by ▴ 40
3
votes
11
replies
17k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq deseq2
updated 6.5 years ago by 33k • written 6.5 years ago by ▴ 20
2
votes
18
replies
16k
views
DEseq2 time-series design.
deseq2 timecourse design
updated 2.1 years ago by • 0 • written 6.7 years ago by ▴ 90
3
votes
14
replies
16k
views
Normalization in DESeq2
deseq2 deseq
updated 6.6 years ago by 33k • written 6.6 years ago by ▴ 70
13
votes
9
replies
16k
views
DESeq2 and shrinkage of log2 fold changes
deseq2
updated 6 months ago by 33k • written 5.5 years ago by ▴ 90
9
votes
6
replies
16k
views
DESEq2 comparison with mulitple cell types under 2 conditions
deseq2 multiple factor design
updated 6.2 years ago by 33k • written 6.2 years ago by ▴ 40
5
votes
6
replies
15k
views
Group comparison in DESeq2
deseq2 results
updated 5.9 years ago by 33k • written 5.9 years ago by ▴ 20
4
votes
4
replies
15k
views
Report and compare log2FC vs FC
deseq2 logfc
updated 6.3 years ago by ▴ 10 • written 6.3 years ago by ▴ 60
7
votes
8
replies
15k
views
Integrating DESeq2 and TopGO for Enrichment
go deseq2 rnaseq r
updated 6.5 years ago by ▴ 600 • written 6.5 years ago by ▴ 20
20
votes
12
replies
14k
views
New function lfcShrink() in DESeq2
deseq2
updated 23 months ago by • 0 • written 4.2 years ago by 33k
0
votes
9
replies
13k
views
logfoldStandard Error and wald-statistics in DESeq2 results
deseq2 wald
updated 6.4 years ago by 33k • written 6.4 years ago by ▴ 10
13
votes
4
replies
13k
views
Dealing with genes that have Padj=NA
deseq2
updated 3.0 years ago by ▴ 10 • written 5.6 years ago by ▴ 50
7
votes
15
replies
13k
views
DESEq2 Paired samples Before and after treatment
deseq2 paired samples
5.1 years ago adesrichard ▴ 20
0
votes
4
replies
13k
views
3D PCA Plot of RNA-seq Data using plotPCA from within DESeq2
deseq2 rnaseq PCA
updated 6.3 years ago by 33k • written 6.3 years ago by ▴ 50
1
vote
10
replies
12k
views
Inputting counts of zero into DESeq2
deseq2
updated 6.1 years ago by ▴ 10 • written 6.7 years ago by ▴ 10
2
votes
3
replies
12k
views
Removing genes with very low counts in all samples before run DESeq
deseq2 statistical power independent filtering
6.7 years ago alejandro.colaneri ▴ 20
1
vote
7
replies
12k
views
getting error with DEseq2
deseq2
5.2 years ago Nemo ▴ 80
11
votes
17
replies
12k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
written 6.8 years ago by ▴ 120
23
votes
22
replies
12k
views
DESeq2 for ChIP-seq differential peaks
deseq2 deseq chipseq
updated 4.1 years ago by ▴ 100 • written 5.9 years ago by ▴ 170
1
vote
3
replies
11k
views
log2FoldChange calculation in DESeq2 output
deseq2
updated 5.5 years ago by 33k • written 5.5 years ago by • 0
6
votes
5
replies
11k
views
Installation of package DESeq2
deseq2 rcurl annotate genefilter geneplotter
updated 4.6 years ago by 25k • written 4.6 years ago by ▴ 10
5
votes
14
replies
11k
views
DESeq2 paired multifactor test
deseq2 paired
6.8 years ago • updated 6.7 years ago hwillenbrock ▴ 10
10
votes
1
reply
11k
views
Deseq2: RNA-seq and Negative binomial distribution
rnaseq deseq2
updated 5.7 years ago by 33k • written 5.7 years ago by ▴ 20
2
votes
4
replies
11k
views
DESeq2 FPKM normalization
deseq2 normalization
5.5 years ago ribioinfo ▴ 90
2
votes
5
replies
10k
views
DESeq2: Paired Test
DESeq DESeq2 DESeq DESeq2
7.3 years ago Pankaj Agarwal ▴ 100
26
votes
16
replies
10k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 3.3 years ago by ▴ 10 • written 5.1 years ago by ▴ 170
0
votes
5
replies
10k
views
package DESeq2 installation with R.
deseq2 R package installation
updated 7 weeks ago by 33k • written 3.4 years ago by • 0
3
votes
6
replies
10k
views
Unable to load library DESeq2 (installation of package had non-zero exit status)
DESeq2
updated 3.2 years ago by 33k • written 3.2 years ago by ▴ 40
18
votes
24
replies
10k
views
[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 5 months ago by • 0 • written 6.4 years ago by ▴ 100
4
votes
8
replies
9.9k
views
What is colData? How do I make one?
deseq2 coldata
updated 2.7 years ago by ▴ 800 • written 2.7 years ago by ▴ 10
3
votes
2
replies
9.7k
views
DEseq2 - Use normalized DEseq2 counts to plot most expressed genes per group
deseq2 R rnaseq
updated 5.6 years ago by 33k • written 5.6 years ago by • 0
1
vote
1
reply
9.3k
views
Deseq2 for RNAseq experiments without replicates
rnaseq deseq2
updated 5.5 years ago by 33k • written 5.5 years ago by • 0
15
votes
8
replies
9.3k
views
DESeq2 - Acquiring batch-corrected values for PCA and hierarchical clustering
deseq2 deseq
6.7 years ago salahm ▴ 70
8
votes
8
replies
9.1k
views
Heatmap from DESeq2 DE genes
deseq2 heatmap
updated 6.5 years ago by 57k • written 6.5 years ago by ▴ 60
22
votes
7
replies
9.1k
views
Usability of ERCC spike-ins in standard RNAseq experiments
RNAseq deseq2 ercc
updated 4.8 years ago by ★ 3.7k • written 4.8 years ago by ▴ 20
9
votes
9
replies
9.0k
views
How does DESeq2 handle zero counts in one condition?
deseq2 deseq rna-seq
6.6 years ago gavrielmatt • 0
7
votes
3
replies
8.7k
views
DESeq2: multiple conditions design -- How to select subset comparisons from the DESeq object for PCA, ...
deseq2
updated 4.5 years ago by • 0 • written 5.4 years ago by ▴ 20
2
votes
3
replies
8.6k
views
DESeq2: multiple factors and comparison of a main factor between samples
deseq2 multiple factor design
updated 6.3 years ago by 33k • written 6.3 years ago by ▴ 80
2
votes
6
replies
8.6k
views
DESeq2 vs limma/voom: PCA completely different. How to proceed?
limma DESeq2 limma DESeq2
updated 8.3 years ago by ★ 3.7k • written 8.3 years ago by ▴ 270
5
votes
11
replies
8.5k
views
DESeq2: with multiple factors and interaction terms won't show all effects
deseq2 multiple factor design contrast interactions
updated 6.4 years ago by 33k • written 6.4 years ago by ▴ 80
1
vote
5
replies
8.5k
views
How do I extract the principal components in DESeq2?
deseq2 pca
updated 6.1 years ago by 33k • written 6.1 years ago by ▴ 10
1
vote
1
reply
8.4k
views
Undertanding how DESeq2 handles multiple test conditions
rnaseq deseq2 r
updated 6.5 years ago by 7.6k • written 6.5 years ago by ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: An error using Diffbind plotprofile by doug.barrows • 0
Hi there, it's hard to tell how to debug without having the data. Could you potentially send me the object you are attempting to use for th…
Comment: DESeq2 Shrinkage methods for scRNA-Seq by Pedro Tan • 0
Thanks Michael! I will stick to apeglm and incorporate alternate size factors for single cell data. All the best, Pedro
Answer: Macbook M1 install genefilter failed by soda ▴ 10
i have solved this problem by myself. share with you. you need to download gfortran in path /opt/R/arm64/bin this website helped me: **h…
Comment: Best practice for quantifying sncRNA by James W. MacDonald 57k
If you used the QIASeq miRNA library, then you are wasting your time. That library adds the UMI barcodes and is intended for you to then up…
Answer: BioCAsia Virtual Meeting, 15-18 October 2020 by Cassandra Holmes • 0
All the types of bio-conductors are presented to the buyers. The change of the [proposal writing help][1] is ensured for the users. The bio…
Votes
Answer: Macbook M1 install genefilter failed
BioCAsia Virtual Meeting, 15-18 October 2020
Answer: Selecting pairs of exons from differentially spliced genes
Comment: Idea: Using DESeq2 to test a change in ratio of two genes
Time Series Analysis
Awards • All
Popular Question to Gordon Smyth 43k
Teacher to JP Carter ▴ 40
Popular Question to amalthomas111 • 0
Scholar to gabriel.hoffman ▴ 90
Popular Question to Thomas Maurel ▴ 790
Locations • All
Japan, 3 minutes ago
United States, 4 minutes ago
United States, 11 minutes ago
United States, 15 minutes ago
San Diego, 21 minutes ago
Traffic: 458 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6