Showing : deseq2 • reset
13
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22
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27k
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DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 10 weeks ago by 41k • written 7.9 years ago by ▴ 30
0
votes
7
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438
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DESeq2 filtering vs edgeR filtering
DESeq2
7 weeks ago • updated 5 weeks ago fr8712ca-s • 0
0
votes
4
replies
744
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
11 months ago sreeshmaraj72 • 0
4
votes
13
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1.4k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 41k • written 8 months ago by • 0
14
votes
5
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22k
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Dealing with genes that have Padj=NA
deseq2
updated 9 months ago by • 0 • written 8.4 years ago by ▴ 60
0
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11
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1.3k
views
Unable to install DESeq2
DESeq2
updated 9 months ago by 65k • written 9 months ago by • 0
1
vote
9
replies
5.3k
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how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 6.2 years ago by • 0
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 10 months ago by ▴ 20 • written 18 months ago by ▴ 20
2
votes
6
replies
354
views
Factor vs Character in design
DESeq2
8 weeks ago James Aiden • 0
0
votes
6
replies
861
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
0
votes
5
replies
709
views
Wondering how to look at the reads of a gene in samples to check if it was knocked out?
knockout DESeq2
written 10 months ago by • 0
1
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3
replies
600
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 4 months ago by • 0
1
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2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
0
votes
3
replies
460
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
1
vote
3
replies
898
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Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue Spati RSEM deno DEseq2
updated 10 months ago by • 0 • written 12 months ago by • 0
8
votes
12
replies
2.6k
views
DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
DESeq2
updated 12 months ago by 41k • written 12 months ago by ▴ 90
5
votes
18
replies
7.5k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor Install DESeq2
updated 4 months ago by • 0 • written 2.3 years ago by • 0
3
votes
2
replies
563
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 5 months ago by 65k • written 5 months ago by • 0
0
votes
2
replies
550
views
Accounting for technical replicates in DESeq2
DESeq2
updated 11 months ago by ★ 1.3k • written 11 months ago by • 0
1
vote
8
replies
2.8k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.2 years ago by ▴ 60
0
votes
5
replies
545
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Unexpected results for a differential expression analysis between males and females
DESeq2
updated 4 months ago by ★ 3.3k • written 4 months ago by • 0
1
vote
3
replies
474
views
DESeq2: the model matrix is not full rank issue
DESeq2
updated 4 months ago by • 0 • written 4 months ago by • 0
0
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2
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104
views
DESeq2 v1.35.0
DESeq2
updated 4 days ago by 41k • written 4 days ago by • 0
0
votes
2
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1.4k
views
about baseMean in DEseq2
DESeq2
written 2.8 years ago by ▴ 670
0
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17
replies
3.4k
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What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 10 months ago by • 0 • written 6.6 years ago by • 0
0
votes
4
replies
688
views
Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink DESeq2
written 4 months ago by • 0
2
votes
6
replies
3.0k
views
DESeq2 Dispersion Per Condition
deseq2
updated 9 months ago by • 0 • written 8.1 years ago by ▴ 20
2
votes
2
replies
314
views
locfunc not found in DESeq2
locfunc DESeq2 shorth estimateSizeFactors
10 weeks ago Hope ▴ 10
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 6 months ago by • 0 • written 6.5 years ago by ▴ 60
0
votes
2
replies
559
views
Heat Map
ColData pheatmap DESeq2
written 10 months ago by • 0
0
votes
2
replies
481
views
plotCounts label each sample
p DESeq2
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
1
vote
3
replies
1.7k
views
How does DESeq2 calculate FPKM values when gene lengths are not supplied?
deseq2
written 4.1 years ago by • 0
0
votes
6
replies
207
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 2 days ago by ★ 1.3k • written 4 days ago by ▴ 130
0
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2
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317
views
Complex DESeq2 Experimental Design
DESEq2 DESeq2
updated 9 months ago by 65k • written 9 months ago by • 0
9
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5
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5.1k
views
Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 5 months ago by 50k • written 8.2 years ago by ▴ 90
0
votes
3
replies
375
views
LOG2FC DESEQ2
DESeq2
updated 3 months ago by 41k • written 3 months ago by • 0
6
votes
19
replies
2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 6 days ago by • 0 • written 4.6 years ago by ▴ 10
1
vote
3
replies
410
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
4
votes
7
replies
873
views
weird volcano plot
DESeq2
updated 8 weeks ago by • 0 • written 5 months ago by ▴ 10
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
10 months ago Ndimensional ▴ 20
0
votes
2
replies
341
views
Running DESeq on normalized data
deseq DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
0
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4
replies
374
views
Extract LRT results for each comparison
LRT DESeq2
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
28
votes
21
replies
48k
views
deseq2 filter the low counts
deseq2 lowcount
updated 3 months ago by • 0 • written 9.2 years ago by ▴ 40
4
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9
replies
1.3k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
3
votes
6
replies
22k
views
Deseq: What does "BaseMean" mean?
deseq2
updated 3 months ago by • 0 • written 5.6 years ago by • 0
0
votes
2
replies
584
views
DESeq2 collinearity, adjusting for covariates, and the ground truth
DESeq2
updated 4 months ago by 41k • written 4 months ago by • 0
0
votes
4
replies
270
views
DEG with low counts
DESeq2
updated 17 days ago by 41k • written 22 days ago by • 0
9
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12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 18 days ago by • 0 • written 8.8 years ago by ▴ 30
2
votes
5
replies
11k
views
Conversion from counts to FPKM
counts fpkm fpkm() normalization deseq2
updated 6 months ago by • 0 • written 5.4 years ago by • 0
2
votes
8
replies
1.1k
views
Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge beta DESeq2
11 months ago • updated 10 months ago Ndimensional ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Comment: Help with running egsea() by James W. MacDonald 65k
I don't understand the last question, but do look at the msigdb.gsets argument to `buildIdx` in the help page for that function.
Answer: Help with running egsea() by James W. MacDonald 65k
There are no arguments to `egsea.base`, as it is meant only as a helper function to return the different methods. In addition, if you are u…
Votes
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
Answer: How to save the DEXSeq results
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