Showing : deseq2 • reset
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DE analysis model matrix for paired samples
NanoStringNCTools DESeq2
updated 1 day ago by 35k • written 2 days ago by ▴ 10
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3
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90
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Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter DifferentialExpression Housekeeping DESeq2 NanoString
updated 1 day ago by 35k • written 2 days ago by • 0
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1
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50
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Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog DESeq2 VST
updated 3 days ago by 35k • written 4 days ago by • 0
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1
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55
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Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 4 days ago by 35k • written 5 days ago by • 0
1
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2
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134
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Use of shrunken LFCs to address questions about the distribution of LFCs between gene categories.
deseq2 apeglm DESeq2
8 days ago • updated 7 days ago i.sudbery ▴ 20
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2
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111
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PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp
DESeq2 PCA
updated 8 days ago by ▴ 970 • written 8 days ago by • 0
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2
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130
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rlog normalised count for comparing gene expression between samples
DESeq2
8 days ago Sam • 0
1
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2
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104
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rlog vs vst for outlier identification
rlog DESeq2 vst outliers
8 days ago Bex • 0
2
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5
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166
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DESeq2 median of ratios normalization for signature score calculation
MRN RNASeq Normalization DESeq2
updated 9 days ago by 35k • written 11 days ago by • 0
2
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3
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117
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Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 9 days ago by 35k • written 10 days ago by ▴ 100
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4
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143
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DESeq treatment over baseline versus placebo over baseline methodology
DESeq2
9 days ago walter.eckalbar • 0
1
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3
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146
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Transformations of the variance in RNA-seq count data DESeq2
RNASeq vst R rlog DESeq2
updated 8 days ago by 35k • written 12 days ago by • 0
1
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2
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139
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DESeq2 expressed gene
DESeq2
11 days ago BioEpi • 0
0
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3
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134
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Same p-adjusted value for all samples
DESeq2 p-adjusted-value Logfoldchange
updated 13 days ago by 35k • written 13 days ago by • 0
4
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5
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197
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Help with droplevels in Deseq2
droplevels DESeq2
updated 13 days ago by ▴ 970 • written 14 days ago by • 0
1
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8
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261
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DESeq2 analysis for targeted RNA-seq
DifferentialExpression DESeq2
15 days ago • updated 13 days ago dadca596 • 0
1
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3
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147
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Adding sample label to PCA plot
plotpca DESeq2
15 days ago • updated 14 days ago bjen731 • 0
3
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5
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496
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P adjusted values in Deseq2
DESeq2 Statistics
written 12 months ago by • 0
1
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1
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85
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TPM to raw counts
salmon DESeq2
updated 15 days ago by 13k • written 15 days ago by • 0
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1
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80
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Removal of sample data which belong to a different experiment
DESeq2
updated 17 days ago by 35k • written 17 days ago by • 0
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3
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172
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DESeq2: model matrix is not full rank
DESeq2
updated 18 days ago by 35k • written 18 days ago by • 0
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69
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Complex design in DESeq2 doesn't seem to be supported in Glimma
limma Glimma RNASeq DESeq2
22 days ago Jonas • 0
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2
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152
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Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch RNASeq BatchEffect DESeq2
updated 19 days ago by 13k • written 23 days ago by • 0
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1
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131
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Is it possible to specify random nested factor in DEseq2?
nested DESeq2
updated 23 days ago by 35k • written 29 days ago by • 0
2
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2
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189
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EdgeR installation issue
limma edgeR DESeq2
24 days ago • updated 23 days ago aonghus • 0
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2
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176
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sigh of log2FC values in DESeq2
sign FoldChange DESeq2 reference
updated 24 days ago by 35k • written 25 days ago by • 0
2
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2
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157
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Ashr and IHW
Ashr LFCShrinkage IHW DESeq2
4 weeks ago • updated 9 days ago Bex • 0
0
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7
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316
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Deseq2 normalization for WGCNA
RNASeq Deseq2 DESeq2 WGCNA
updated 4 weeks ago by 35k • written 4 weeks ago by • 0
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2
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96
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DeSeq2 - design formula for enrichment on combinated conditions AB, not A, not B
conditions design DESeq2 Synergy
updated 4 weeks ago by 35k • written 4 weeks ago by • 0
3
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2
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184
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Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
5 weeks ago mohammedtoufiq91 ▴ 10
3
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2
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177
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P-values change 100-fold with only a single count changed
DESeq2
5 weeks ago • updated 5 days ago Andrey • 0
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1
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116
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Analyzing RNA-seq data with DESeq2 Tutorial - tximeta Package Causing Error in UseMethod("filter_")
tximeta UseMethod("filter_") DESeq2
updated 5 weeks ago by 35k • written 5 weeks ago by • 0
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2
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150
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DESeqDataSet design issue
DESeq DESeq2
5 weeks ago matthew.valentine • 0
2
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1
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144
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Converting vst-normalized gene expression counts back after correcting for tumor purity
Inverse-VST Tumor-Purity VST DESeq2 Normalization
updated 5 weeks ago by 35k • written 5 weeks ago by • 0
0
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1
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131
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RNA-Seq Workflow Vignette - library(airway) Missing "quants" directory
RNASeq DESeq2 airway
updated 5 weeks ago by 35k • written 5 weeks ago by • 0
2
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3
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250
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DESeq2 - batch, condition and tissue information
DESeq2
6 weeks ago • updated 5 weeks ago Ela__77 • 0
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5
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265
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DESeq2 analyze MeRIP-seq
DESeq2 MeRIP-seq
updated 5 weeks ago by 35k • written 6 weeks ago by • 0
1
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2
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192
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Design formula in DESeq2
groups dispersion DESeq2 desing
6 weeks ago m.glymenaki • 0
3
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4
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224
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DESEQ2 Results log2fold and pvalue changes after removing genes
DESeq2
6 weeks ago Bine ▴ 20
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1
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110
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different results between DESeq model with multiple groups or with specific groups
DESeq2
updated 6 weeks ago by 35k • written 6 weeks ago by • 0
0
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1
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126
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Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 6 weeks ago by 35k • written 7 weeks ago by • 0
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3
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177
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Error in DESeq2
DESeq2
updated 6 weeks ago by 35k • written 6 weeks ago by • 0
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2
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255
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deseq2 datasetfrommatrix
DESeq2
updated 7 weeks ago by ▴ 970 • written 7 weeks ago by • 0
1
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1
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162
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Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 7 weeks ago by 35k • written 7 weeks ago by • 0
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1
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154
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Paired sample design in DESeq2
DESeq2
updated 7 weeks ago by 35k • written 7 weeks ago by • 0
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9
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354
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DEseq2 replicate normalization
DEseq2 replicate DESeq2 normalization
7 weeks ago michael.morash • 0
0
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5
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390
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Can I use VST on TPM data? (DESeq2)
DESeq2 VST
updated 6 weeks ago by 35k • written 7 weeks ago by • 0
0
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1
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158
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values (NA) in p value Deseq2 (reopen)
pvalue NA R DESeq2
updated 7 weeks ago by ▴ 970 • written 7 weeks ago by • 0
2
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2
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205
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padjust after running DESEQ2
DESeq2
7 weeks ago Bine ▴ 20
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4
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233
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Normalization by variance stabilizing transformation VST
library composition vst DESeq2 Normalization
7 weeks ago kristoffersandas • 0
50 results • Page 1 of 1
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Comment: DiffBind dba.count Error in if (sum(tokeep) < length(tokeep)) by tjhwangxiong • 0
``` https://drive.google.com/drive/folders/1787thVatZpt_KFrfXY-aXV1m0FRm8Mhm?usp=sharing ``` Thanks for your reply. I have uploaded the fil…
Comment: Trying to follow a gene set analyisis in R by Michael Love 35k
No I can’t help with exercises. Just to be clear I’m not affiliated with Harvard and have no supported effort in relation to the edx classe…
Answer: Problems to find the pvalues via rowttests by Gordon Smyth 44k
Ordinary t-tests aren't recommended for genomic analyses because they have poor power and higher false discovery rates. Using the limma p…
Answer: How to insert a qvalues column in a dataframe with pvalues in R by Gordon Smyth 44k
Here and in a previous post, it seems you're not using recommended Bioconductor workflows for Affymetrix microarrays. If you used a standar…
Comment: Trying to follow a gene set analyisis in R by leonardorosas2001 • 0
Thank you. I hope I can still let you know if I have issues with your exercises. They are very challenging but useful! :)
Votes
Answer: Problems to find the pvalues via rowttests
A: How to use subSeq with DNAStringSet and information of GroupedIRanges?
A: How to use subSeq with DNAStringSet and information of GroupedIRanges?
Annotating GRanges with TxDb gene models using plyranges
plyranges select() when a metadata column is shared with core variable
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