Showing : Deseq2 • reset
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DE analysis model matrix for paired samples
NanoStringNCTools DESeq2
updated 3 hours ago by 35k • written 7 hours ago by ▴ 10
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30
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Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter DifferentialExpression Housekeeping DESeq2 NanoString
updated 11 hours ago by 35k • written 12 hours ago by • 0
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42
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Unusal standard deviation after rlog transformation and the homoscedasticity of the data
rlog DESeq2 VST
updated 1 day ago by 35k • written 2 days ago by • 0
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46
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Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 2 days ago by 35k • written 3 days ago by • 0
1
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2
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118
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Use of shrunken LFCs to address questions about the distribution of LFCs between gene categories.
deseq2 apeglm DESeq2
6 days ago • updated 5 days ago i.sudbery ▴ 20
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2
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103
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PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp
DESeq2 PCA
updated 6 days ago by ▴ 970 • written 6 days ago by • 0
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2
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123
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rlog normalised count for comparing gene expression between samples
DESeq2
6 days ago Sam • 0
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2
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97
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rlog vs vst for outlier identification
rlog DESeq2 vst outliers
6 days ago Bex • 0
2
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5
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163
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DESeq2 median of ratios normalization for signature score calculation
MRN RNASeq Normalization DESeq2
updated 7 days ago by 35k • written 9 days ago by • 0
2
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3
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114
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Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 7 days ago by 35k • written 8 days ago by ▴ 100
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4
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138
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DESeq treatment over baseline versus placebo over baseline methodology
DESeq2
8 days ago • updated 7 days ago walter.eckalbar • 0
1
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3
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143
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Transformations of the variance in RNA-seq count data DESeq2
RNASeq vst R rlog DESeq2
updated 6 days ago by 35k • written 10 days ago by • 0
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2
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136
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DESeq2 expressed gene
DESeq2
9 days ago BioEpi • 0
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3
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130
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Same p-adjusted value for all samples
DESeq2 p-adjusted-value Logfoldchange
updated 11 days ago by 35k • written 11 days ago by • 0
4
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5
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196
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Help with droplevels in Deseq2
droplevels DESeq2
updated 11 days ago by ▴ 970 • written 12 days ago by • 0
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8
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259
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DESeq2 analysis for targeted RNA-seq
DifferentialExpression DESeq2
13 days ago • updated 11 days ago dadca596 • 0
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3
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142
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Adding sample label to PCA plot
plotpca DESeq2
13 days ago • updated 12 days ago bjen731 • 0
3
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5
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494
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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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84
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TPM to raw counts
salmon DESeq2
updated 13 days ago by 13k • written 13 days ago by • 0
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1
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78
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Removal of sample data which belong to a different experiment
DESeq2
updated 15 days ago by 35k • written 15 days ago by • 0
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3
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168
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DESeq2: model matrix is not full rank
DESeq2
updated 16 days ago by 35k • written 16 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
20 days ago Jonas • 0
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2
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147
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Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch RNASeq BatchEffect DESeq2
updated 17 days ago by 13k • written 21 days ago by • 0
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1
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125
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Is it possible to specify random nested factor in DEseq2?
nested DESeq2
updated 21 days ago by 35k • written 27 days ago by • 0
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2
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184
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EdgeR installation issue
limma edgeR DESeq2
22 days ago • updated 21 days ago aonghus • 0
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2
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174
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sigh of log2FC values in DESeq2
sign FoldChange DESeq2 reference
updated 22 days ago by 35k • written 24 days ago by • 0
2
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2
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156
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Ashr and IHW
Ashr LFCShrinkage IHW DESeq2
4 weeks ago • updated 7 days ago Bex • 0
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7
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308
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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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183
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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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173
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P-values change 100-fold with only a single count changed
DESeq2
5 weeks ago • updated 3 days ago Andrey • 0
0
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115
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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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148
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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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142
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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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130
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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
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3
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249
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DESeq2 - batch, condition and tissue information
DESeq2
5 weeks ago Ela__77 • 0
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5
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260
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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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188
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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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222
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DESEQ2 Results log2fold and pvalue changes after removing genes
DESeq2
6 weeks ago Bine ▴ 20
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108
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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
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1
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124
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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 6 weeks ago by • 0
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3
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174
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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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249
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deseq2 datasetfrommatrix
DESeq2
updated 6 weeks ago by ▴ 970 • written 7 weeks ago by • 0
1
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1
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160
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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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153
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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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352
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DEseq2 replicate normalization
DEseq2 replicate DESeq2 normalization
7 weeks ago • updated 6 weeks ago michael.morash • 0
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5
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379
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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
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153
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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
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2
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204
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padjust after running DESEQ2
DESeq2
7 weeks ago Bine ▴ 20
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4
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232
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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
Recent ...
Replies
Comment: Trying to follow a gene set analyisis in R by Michael Love 35k
It looks like you only have a single sample.
Comment: Trying to follow a gene set analyisis in R by leonardorosas2001 • 0
I get the following > design = model.matrix(~ es$condition) > design (Intercept) es$conditiondex4 attr(,"assign") [1] 0 1 attr(,"co…
Comment: How to use subjunc for differential splicing analysis? by Yang Liao ▴ 280
Annotation to the *subjunc* aligner helps the aligner to better map the reads. The aligner generates BAM files, which contains mapped reads…
Answer: universalmotif, question about enrich_motifs function and number of hits returne by btremblay ▴ 30
Hi, After doing some digging I've isolated the issue to being related to the threshold calculation which you request with the `threshold…
Answer: DE analysis model matrix for paired samples by Michael Love 35k
Agree with swbarnes2. It just seems like the condition effect is very small. Also I'd double check the metadata. Sometimes samples are swap…
Votes
A: DNAcopy
Comment: Using DiffBind blacklists and greylists with results mapped to BDGP6
Answer: How to use subjunc for differential splicing analysis?
Answer: catchKallisto results are not counts
Answer: catchKallisto results are not counts
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