Showing : deseq2 • reset
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564
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i'm not getting any differentially expressed genes.
DESeq2
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
2
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1
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782
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Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
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1
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504
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Perform PCA for sample clustering using DESeq2
DESeq2
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
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3
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991
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 21 months ago by • 0
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2
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910
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DESeq2: Comparing A Knockout to a Strain
DESeq2
19 months ago Viktor Thiel • 0
0
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1
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814
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DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2 scCITE-seq
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
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8
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1.4k
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
19 months ago michelafrancesconi8 • 0
0
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1
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646
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Unusually large fold-changes in Deseq2 results
DESeq2
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
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4
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877
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DESeq2 Replicates
DESeq2 RNASeq
19 months ago kcarey • 0
2
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6
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977
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Factor vs Character in design
DESeq2
19 months ago James Aiden • 0
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3
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987
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Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2 glmGamPoi
20 months ago • updated 19 months ago I-Hsuan Lin ▴ 10
4
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7
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1.8k
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weird volcano plot
DESeq2
updated 19 months ago by • 0 • written 23 months ago by ▴ 10
0
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1
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696
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DEseq2 dispersion plot
DESeq2
updated 19 months ago by 43k • written 20 months ago by • 0
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3
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1.0k
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 20 months ago by ★ 1.4k • written 20 months ago by ▴ 10
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2
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1.0k
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Is DESeq2 normalisation appropriate when counts were obtained for a small number of genes?
DESeq2
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
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3
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868
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Would I treat surrogate variables as batches?
DESeq2 sva
updated 20 months ago by 68k • written 20 months ago by ▴ 10
0
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1
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651
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Changed DESeq2 comparison value but the heatmap is still the same
DESeq2 pheatmap
updated 20 months ago by 68k • written 20 months ago by • 0
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4
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967
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Further clarification of unbalanced group sizes DESeq2
DESeq2
20 months ago hmillike • 0
0
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1
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455
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few significant genes from DESeq2 analysis
DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
1
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4
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1.4k
views
DEseq2 coefficient
DESeq2 coefficient
20 months ago • updated 18 months ago JKim • 0
3
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5
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1.7k
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 20 months ago by 43k • written 20 months ago by ▴ 10
2
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1
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717
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Limma Question
DESeq2 BatchEffect limma RNASeq
updated 20 months ago by 43k • written 20 months ago by ▴ 10
2
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2
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801
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locfunc not found in DESeq2
locfunc DESeq2 shorth estimateSizeFactors
20 months ago Hope ▴ 10
1
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2
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823
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evaluate the variable importance on genes
DESeq2 deseq
20 months ago Meme • 0
0
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3
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799
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library sizes differ extremely after dds
DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
1
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4
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1.5k
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Comparing gene expression across three tissue types to identify any difference.
DESeq2
20 months ago James Aiden • 0
0
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13
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1.8k
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Unexpected behavior of lfcShrink() function in DESeq2 analysis
DESeq2 SmallRNA
updated 20 months ago by 43k • written 20 months ago by • 0
1
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5
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953
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vst transformation and zero counts
DESeq2
updated 20 months ago by ★ 5.0k • written 20 months ago by ▴ 740
1
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12
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2.6k
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How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison DESeq2 InteractionSet pvalue
20 months ago paria.alipour • 0
0
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3
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1.3k
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utf-8 codec can't decode byte 0xd5
importr DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
0
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1
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466
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Problems with filtering DESeq Results (log2fold change)
DESeq2
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
0
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3
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1.1k
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DESeq2: Adjust for treatment effect patient vs control
DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
0
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1
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1.8k
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Pseudobulk-DESeq2 analyze multiple cell types at once?
pseudobulk DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
0
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7
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1.3k
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DESeq filtering specific to contrasts
DESeq2
updated 18 months ago by 43k • written 20 months ago by • 0
0
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2
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826
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help checking the design matrix and contrast in DESeq2 "not full rank" scenario
DESeq2
20 months ago ccshao ▴ 70
0
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1
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643
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Double batch effect (Individuals nested within blocks in DESeq2)
DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
1
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2
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918
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DESeq2 issue: can't create DESeq2 object
DESeq2 RBioinf
20 months ago Magdalena • 0
0
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1
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441
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Inconsistency in DESeq2 Log fold change
DESeq2
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
0
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3
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741
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DESeq2 Results in Different Pvalue & Log2FC using the same code and data
DESeq2 dese
written 20 months ago by • 0
0
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5
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1.1k
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DESEQ2 Repeated Measures-like design error help
DESeq2
updated 20 months ago by 43k • written 20 months ago by ▴ 10
0
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3
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1.0k
views
DESeq2 interaction terms RIPseq analysis
DESeq2 RIPSeq
updated 20 months ago by 43k • written 20 months ago by • 0
2
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2
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1.7k
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
20 months ago jackafiore • 0
4
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2
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2.6k
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How to do DESeq2 on Kallisto Data
DESeq2 Kallisto
updated 20 months ago by ▴ 40 • written 20 months ago by • 0
1
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2
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2.4k
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.5 years ago by • 0
0
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2
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712
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Pairwise analysis of DESeq result and limma result
DESeq2 limma
20 months ago Lily Cheang ▴ 10
0
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4
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844
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DESeq2 nomalize value
DESeq2
20 months ago 史哲 • 0
0
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4
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1.8k
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Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink DESeq2
written 22 months ago by • 0
2
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1
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706
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 21 months ago by 43k • written 21 months ago by ▴ 20
0
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3
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1.0k
views
LOG2FC DESEQ2
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
0
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1
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421
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unequal number of treatmets to control
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
4,835 results • Page 7 of 97
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Answer: Using DESeq2 for age prediction by ATpoint ★ 5.0k
The package has no such inbuilt function but you are free to use the vst (or any normalized) counts to train a regression model or classifi…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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