Showing : DEseq2 • reset
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Deseq2 Design
RNASeq DESeq2
updated 1 day ago by 67k • written 1 day ago by • 0
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5
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252
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p value is 0, padj is 0
DESeq2
2 days ago • updated 1 day ago Wirayatida • 0
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56
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
1 day ago • updated 23 hours ago bbao • 0
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2
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281
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
2 days ago georgii.vdovin • 0
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67
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
3 days ago txema.heredia • 0
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7
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615
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 3 days ago by • 0 • written 5 days ago by • 0
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223
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 7 days ago by 43k • written 7 days ago by ▴ 20
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3
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314
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DESeq2 - Comparing Comparisons
DESeq2
updated 2 days ago by 67k • written 9 days ago by • 0
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4
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429
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lfcShrink and alpha value
lfcShrink DESeq2
15 days ago • updated 9 days ago cropero • 0
1
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1
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202
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 11 days ago by 43k • written 18 days ago by • 0
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2
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134
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 11 days ago by 43k • written 12 days ago by • 0
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2
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180
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
17 days ago • updated 16 days ago Anna • 0
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2
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498
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Deseq2 res Function
DESeq2
updated 19 days ago by 67k • written 20 days ago by ▴ 10
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4
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377
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
21 days ago NB • 0
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5
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357
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Identical samples after deseq2 batch effect removal
DESeq2
updated 22 days ago by 43k • written 23 days ago by • 0
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211
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 22 days ago by 67k • written 22 days ago by • 0
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270
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
24 days ago • updated 23 days ago Denise • 0
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130
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eRNAs count
RNASeq DESeq2
updated 26 days ago by ★ 4.6k • written 26 days ago by • 0
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1
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379
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DESeq2 rerun returns different results
DESeq2
updated 29 days ago by ★ 4.6k • written 29 days ago by • 0
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1
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217
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 4 weeks ago by 43k • written 4 weeks ago by • 0
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1
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183
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 4 weeks ago by ★ 4.1k • written 4 weeks ago by • 0
2
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2
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578
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Handling biological replicates in DESeq2
DESeq2
updated 4 weeks ago by ★ 4.6k • written 4 weeks ago by • 0
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2
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25k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 5.9 years ago by ▴ 30
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6
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936
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 5 weeks ago by 43k • written 5 weeks ago by ▴ 10
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358
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 5 weeks ago by • 0
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
5 weeks ago LuciaNhu • 0
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380
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Average expression of genes across replicates
DESeq2
updated 5 weeks ago by ★ 4.6k • written 6 weeks ago by • 0
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124
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
6 weeks ago info ▴ 10
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10
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1.3k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
6 weeks ago • updated 5 weeks ago Denise • 0
0
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1
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336
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Deseq to output continous sequencing data
DESeq2
updated 6 weeks ago by 43k • written 9 weeks ago by • 0
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4
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797
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Adjusted p-values become NA when sub-setting samples
DESeq2
9 weeks ago • updated 5 weeks ago txema.heredia • 0
3
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3
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882
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 6 weeks ago by • 0
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2
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345
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 7 weeks ago by • 0
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285
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Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 7 weeks ago by 43k • written 7 weeks ago by • 0
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Analysis of large RNA-Seq Datasets
DESeq2
updated 8 weeks ago by 43k • written 8 weeks ago by • 0
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4
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748
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DESeq2 - interactions when using factors concatenated into group
DESeq2
8 weeks ago • updated 7 weeks ago boczniak767 ▴ 740
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197
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
8 weeks ago JY • 0
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282
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How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 8 weeks ago by 43k • written 8 weeks ago by • 0
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207
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how to extract expression matrix post deseq2
DESeq2
written 8 weeks ago by • 0
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2
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206
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Using Normalized Counts in DESeq2
DESeq2
updated 8 weeks ago by 43k • written 8 weeks ago by • 0
1
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2
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256
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When running contrasts, does it use normalized read counts?
DESeq2
8 weeks ago Katherine • 0
0
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1
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206
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How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 8 weeks ago by ★ 1.4k • written 9 weeks ago by • 0
3
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4
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502
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
9 weeks ago Eva ▴ 10
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4
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495
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Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 8 weeks ago by ★ 4.6k • written 10 weeks ago by • 0
0
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1
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185
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
3
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11
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747
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 9 weeks ago by • 0
2
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4
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419
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
9 weeks ago jihoon.kim.1495 ▴ 10
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6
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825
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 7 weeks ago by 43k • written 9 weeks ago by • 0
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4
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457
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 9 weeks ago by ★ 4.6k • written 10 weeks ago by • 0
0
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2
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289
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
10 weeks ago • updated 9 weeks ago paul.meraner • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Easiest way to convert read10xMolInfo data into a dataframe in R with gene label by daldabrown9 • 0
For more info visit us on [R350 status check][1] [1]: https://sassagrantstatuscheck.co.za/
Answer: Margins for gene_set_enrichment_plot by Leonardo Collado Torres ★ 1.1k
Hi, In version 1.19.4 of `spatialLIBD` @lahuuki re-implemented the `gene_set_enrichment_plot()` function using `ComplexHeatmap::Heatmap(…
Comment: miRTarRnaseq library by mercedeh.movassagh ▴ 20
Maria please read the mirTarRnaSeq paper. In particular, Supplemental Table 2, clarifies all the statistical models, inputs and outputs. If…
Comment: Help using rtracklayer for gene ID extraction by James W. MacDonald 67k
Telling me you can't do something without showing what you tried is not helpful. When posting here, try to put yourself in the shoes of peo…
Comment: miRTarRnaseq library by María Calvo • 0
Hello Mercedeh, excuse me for not explaining it adecuately, Im using the "Part3 - Identify significant miRNA mRNA relationships for 2 time …
Votes
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
Answer: Mapping Between GenBank ID's and Uniprot
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