Showing : DESeq2 • reset
13
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22
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26k
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DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 8 weeks ago by 41k • written 7.8 years ago by ▴ 30
0
votes
7
replies
406
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DESeq2 filtering vs edgeR filtering
DESeq2
6 weeks ago • updated 29 days ago fr8712ca-s • 0
0
votes
4
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732
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problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
11 months ago sreeshmaraj72 • 0
1
vote
9
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5.2k
views
how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 6.1 years ago by • 0
14
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5
replies
22k
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Dealing with genes that have Padj=NA
deseq2
updated 8 months ago by • 0 • written 8.4 years ago by ▴ 60
0
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11
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1.3k
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Unable to install DESeq2
DESeq2
updated 9 months ago by 65k • written 9 months ago by • 0
4
votes
13
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1.3k
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Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 41k • written 8 months ago by • 0
8
votes
7
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1.7k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 9 months ago by ▴ 20 • written 18 months ago by ▴ 20
2
votes
6
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325
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Factor vs Character in design
DESeq2
7 weeks ago James Aiden • 0
0
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6
replies
808
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
0
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5
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696
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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
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569
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 4 months ago by • 0
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 11 months ago by • 0
0
votes
3
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439
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago • updated 4 months ago Karthik • 0
1
vote
3
replies
871
views
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 11 months ago by • 0
8
votes
12
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2.5k
views
DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
DESeq2
updated 11 months ago by 41k • written 12 months ago by ▴ 90
5
votes
18
replies
7.4k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor Install DESeq2
updated 4 months ago by • 0 • written 2.2 years ago by • 0
0
votes
3
replies
359
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 11 weeks ago by • 0
0
votes
2
replies
539
views
Accounting for technical replicates in DESeq2
DESeq2
updated 11 months ago by ★ 1.3k • written 11 months ago by • 0
1
vote
8
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2.7k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.1 years ago by ▴ 60
0
votes
5
replies
516
views
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
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444
views
DESeq2: the model matrix is not full rank issue
DESeq2
updated 4 months ago by • 0 • written 4 months ago by • 0
1
vote
8
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1.5k
views
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression DESeq2
written 10 months ago by • 0
0
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2
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1.4k
views
about baseMean in DEseq2
DESeq2
written 2.7 years ago by ▴ 670
0
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17
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3.4k
views
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
655
views
Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink DESeq2
written 4 months ago by • 0
3
votes
2
replies
546
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 4 months ago by 65k • written 4 months ago by • 0
2
votes
2
replies
293
views
locfunc not found in DESeq2
locfunc DESeq2 shorth estimateSizeFactors
8 weeks ago Hope ▴ 10
0
votes
9
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2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 5 months ago by • 0 • written 6.5 years ago by ▴ 60
0
votes
2
replies
539
views
Heat Map
ColData pheatmap DESeq2
written 10 months ago by • 0
2
votes
8
replies
1.0k
views
Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge beta DESeq2
10 months ago Ndimensional ▴ 20
1
vote
3
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1.7k
views
How does DESeq2 calculate FPKM values when gene lengths are not supplied?
deseq2
written 4.1 years ago by • 0
0
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2
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310
views
Complex DESeq2 Experimental Design
DESEq2 DESeq2
updated 9 months ago by 65k • written 9 months ago by • 0
0
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2
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327
views
Running DESeq on normalized data
deseq DESeq2
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
2
votes
6
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3.0k
views
DESeq2 Dispersion Per Condition
deseq2
updated 9 months ago by • 0 • written 8.0 years ago by ▴ 20
0
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3
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350
views
LOG2FC DESEQ2
DESeq2
updated 11 weeks ago by 41k • written 11 weeks ago by • 0
9
votes
5
replies
5.1k
views
Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 4 months ago by 50k • written 8.2 years ago by ▴ 90
6
votes
16
replies
2.2k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day ago by 41k • written 4.6 years ago by ▴ 10
4
votes
7
replies
838
views
weird volcano plot
DESeq2
updated 7 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
9 months ago Ndimensional ▴ 20
0
votes
2
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463
views
plotCounts label each sample
p DESeq2
updated 10 months ago by ★ 4.0k • written 10 months ago by • 0
0
votes
4
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358
views
Extract LRT results for each comparison
LRT DESeq2
updated 6 months ago by ★ 4.0k • written 6 months ago by • 0
28
votes
21
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48k
views
deseq2 filter the low counts
deseq2 lowcount
updated 3 months ago by • 0 • written 9.2 years ago by ▴ 40
4
votes
9
replies
1.2k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
3
votes
6
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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
557
views
DESeq2 collinearity, adjusting for covariates, and the ground truth
DESeq2
updated 4 months ago by 41k • written 4 months ago by • 0
0
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4
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229
views
DEG with low counts
DESeq2
updated 5 days ago by 41k • written 10 days ago by • 0
9
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12
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7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 6 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
0
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2
replies
612
views
Why my log2fcs are too high?
DESeq2 SingleCell log2FC
12 months ago paria.alipour • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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