Showing : DESeq2 • reset
45
votes
20
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28k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 5.6 years ago by • 0 • written 6.1 years ago by ▴ 100
28
votes
17
replies
9.1k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
7.3 years ago • updated 5.8 years ago Michael Love 35k
27
votes
16
replies
11k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 3.7 years ago by ▴ 10 • written 5.5 years ago by ▴ 170
25
votes
11
replies
6.0k
views
Normalization methodology in DESeq/DESeq2 vs edgeR
deseq deseq2 edgeR normalization
updated 6.2 years ago by ★ 3.7k • written 6.2 years ago by ▴ 70
23
votes
22
replies
12k
views
DESeq2 for ChIP-seq differential peaks
deseq2 deseq chipseq
updated 4.6 years ago by ▴ 100 • written 6.4 years ago by ▴ 170
22
votes
7
replies
9.8k
views
Usability of ERCC spike-ins in standard RNAseq experiments
RNAseq deseq2 ercc
updated 5.3 years ago by ★ 3.7k • written 5.3 years ago by ▴ 20
21
votes
14
replies
29k
views
deseq2 filter the low counts
deseq2 lowcount
updated 11 months ago by 35k • written 6.9 years ago by ▴ 30
20
votes
7
replies
4.3k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma deseq2 edger rnaseq
updated 4.3 years ago by 44k • written 4.3 years ago by • 0
20
votes
12
replies
16k
views
New function lfcShrink() in DESeq2
deseq2
updated 2.4 years ago by • 0 • written 4.7 years ago by 35k
18
votes
24
replies
11k
views
[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 11 months ago by • 0 • written 6.9 years ago by ▴ 110
18
votes
12
replies
2.3k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR deseq2 rna-seq independent filtering
updated 6.6 years ago by 35k • written 6.6 years ago by 7.7k
17
votes
17
replies
3.5k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 7 months ago by 35k • written 3.6 years ago by ▴ 20
16
votes
40
replies
3.0k
views
Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 14 days ago by • 0 • written 2.5 years ago by ▴ 50
16
votes
4
replies
23k
views
FDR and padj in deseq and edger
deseq2 edger
updated 6.2 years ago by 44k • written 6.2 years ago by ▴ 60
16
votes
9
replies
4.4k
views
Diffbind: edgeR or DESeq2 ?
diffbind medip-seq edger deseq2
updated 4.2 years ago by ★ 4.3k • written 5.8 years ago by ▴ 60
15
votes
8
replies
9.5k
views
DESeq2 - Acquiring batch-corrected values for PCA and hierarchical clustering
deseq2 deseq
7.2 years ago salahm ▴ 70
15
votes
3
replies
21k
views
DESeq2: Is it possible to convert read counts to expression values via TPM and return these values?
deseq2 r
updated 5.0 years ago by 35k • written 5.0 years ago by ▴ 40
15
votes
4
replies
1.7k
views
Using multiple tools for differential gene expression analysis as validation
edger limma deseq2 rnaseq
updated 5.6 years ago by 7.7k • written 5.6 years ago by ▴ 130
15
votes
12
replies
1.5k
views
ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like they should be markers
deseq2 ZINB-WaVE single cell RNA-seq differential expression
updated 3.4 years ago by 35k • written 3.4 years ago by ▴ 60
14
votes
19
replies
7.5k
views
DESeq2 Model Design
DESeq2 linear model model
updated 8 months ago by 35k • written 7.2 years ago by ▴ 360
14
votes
7
replies
3.2k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 5.6 years ago by 7.7k • written 5.6 years ago by • 0
14
votes
7
replies
6.9k
views
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
deseq2 ensembl
updated 4.0 years ago by 58k • written 4.0 years ago by ▴ 130
14
votes
9
replies
18k
views
DESeq2 and shrinkage of log2 fold changes
deseq2
updated 12 months ago by 35k • written 6.0 years ago by ▴ 100
13
votes
12
replies
45k
views
[DESEQ2] How to access the normalized data of a DESeqDataSet
deseq2
updated 6.8 years ago by 13k • written 6.8 years ago by ▴ 110
13
votes
4
replies
14k
views
Dealing with genes that have Padj=NA
deseq2
updated 3.5 years ago by ▴ 10 • written 6.1 years ago by ▴ 50
13
votes
16
replies
3.4k
views
Using edgeR or DESeq2 to analyze allele-specific expression?
edgeR deseq2 ase allele
6.3 years ago trianglescout ▴ 40
13
votes
10
replies
2.7k
views
Big differences in logfoldchange for some genes between edgeR and DESeq2
edger deseq2
updated 6.1 years ago by 44k • written 6.1 years ago by • 0
13
votes
6
replies
4.8k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 4.3 years ago by 58k • written 4.3 years ago by ▴ 20
12
votes
7
replies
7.8k
views
DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2 lfc coef contrast
updated 4.5 years ago by 35k • written 4.5 years ago by ▴ 10
12
votes
11
replies
2.6k
views
Memory usage for bplapply -- is the entire environment copied over to each worker thread?
bplapply biocparallel deseq2
updated 6.5 years ago by ★ 6.7k • written 6.5 years ago by ▴ 40
12
votes
6
replies
2.3k
views
Allele Specific Expression in DESeq2 or EdgeR
rnaseq deseq2 edger
6.2 years ago martiningi ▴ 40
12
votes
5
replies
23k
views
plotPCA - how to add labels to a PCA plot
plotPCA deseq2 labels
updated 5.0 years ago by ▴ 130 • written 5.0 years ago by ▴ 50
12
votes
8
replies
1.1k
views
DESeq fitted values using coefficients vs mu
deseq2
updated 5.0 years ago by 35k • written 5.0 years ago by ▴ 830
11
votes
8
replies
6.4k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA RNA-Seq DESeq2 voom removebatcheffect()
updated 5.3 years ago by ★ 2.6k • written 5.3 years ago by ▴ 70
11
votes
10
replies
2.0k
views
Is it appropriate to use DESeq2 to analyse MinION data that's been mapped to a transcriptome?
deseq2 nanopore
2.7 years ago David Eccles (gringer) ▴ 30
11
votes
15
replies
36k
views
DESeq2 output explanation
deseq deseq2
updated 10 weeks ago by 35k • written 7.2 years ago by ▴ 70
11
votes
17
replies
13k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
written 7.2 years ago by ▴ 120
11
votes
1
reply
4.2k
views
identifying the samples on plotPCA
deseq2 plotpca PCa
updated 4.2 years ago by 35k • written 4.2 years ago by ▴ 60
10
votes
14
replies
2.3k
views
Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma edger deseq deseq2
updated 4.3 years ago by 44k • written 4.3 years ago by ▴ 70
10
votes
19
replies
3.1k
views
Macbook M1 install genefilter failed
DESeq2 m1 macbook genefilter
updated 8 weeks ago by ▴ 10 • written 5 months ago by ▴ 80
10
votes
1
reply
11k
views
Deseq2: RNA-seq and Negative binomial distribution
rnaseq deseq2
updated 6.2 years ago by 35k • written 6.2 years ago by ▴ 20
10
votes
9
replies
9.8k
views
How does DESeq2 handle zero counts in one condition?
deseq2 deseq rna-seq
7.0 years ago gavrielmatt ▴ 10
10
votes
9
replies
1.1k
views
Overriding of shrinkage in DESeq2
deseq2
updated 5.8 years ago by 35k • written 5.8 years ago by ▴ 70
10
votes
7
replies
9.9k
views
DESeq2: multiple conditions design -- How to select subset comparisons from the DESeq object for PCA, ...
deseq2
updated 11 weeks ago by 35k • written 5.8 years ago by ▴ 20
10
votes
9
replies
8.3k
views
DESeq2 baseMean values for each sample
deseq2
7.1 years ago aburkha69 ▴ 30
10
votes
6
replies
2.7k
views
Log2FoldChange shrinkage method in DESeq2
deseq2 apeglm lfcshrink
updated 3.7 years ago by 35k • written 3.7 years ago by ▴ 90
10
votes
6
replies
3.3k
views
Bootstrap confidence intervals on RNA-seq expression from Kallisto
rnaseq deseq2 edger voom limma
updated 4.3 years ago by ▴ 90 • written 6.6 years ago by 21k
10
votes
14
replies
7.0k
views
Is there a conceptual difference between vst/rlog transforms and lfcShrink?
deseq2
updated 4.0 years ago by 35k • written 4.0 years ago by ▴ 30
9
votes
14
replies
5.7k
views
too many genes with low read-counts as differential expressed in DESeq2
deseq2 rna-seq
5.5 years ago • updated 5.4 years ago anand_mt ▴ 80
9
votes
7
replies
8.1k
views
What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
deseq2 rnaseq pca tsne
updated 4.6 years ago by ▴ 10 • written 4.6 years ago by ▴ 30
50 results • Page 1 of 1
Recent ...
Replies
Answer: Change the interval of bed file by James W. MacDonald 58k
How about ``` > library(GenomicRanges) ## reproducibility > set.seed(0xabeef) ## fake GRranges with scores > gr <- GRanges(rep("chr…
Comment: Uniform window size for different genes by James W. MacDonald 58k
OK, maybe I don't understand at all. From your original post I thought you wanted a single representative 'gene' rather than all the transc…
Comment: Uniform window size for different genes by rbenel ▴ 20
I tried some workaround, displaying the same gene on both tracks and playing with the `heights` but I still can't get the gene model to be …
Comment: Limma prametrization by Giovanni • 0
Thank you!
Answer: Gviz DataTrack data transformation on the fly by Robert Ivanek ▴ 710
Hi Robert, There was before only implementation of `mean` in aggregation for `window=-1`. This is now fixed in release (1.38.2) and dev…
Votes
A: How to get all possible comparisons in DiffBind
Answer: Limma prametrization
Comment: Limma prametrization
A: Use of pseudoalignment estimated counts as input to edgeR and Limma-Voom
Answer: Unable to GetGRangesFromEnsDb
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