Showing : DESEQ2 • reset
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DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 22 hours ago by ★ 4.8k • written 1 day ago by • 0
4
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6
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1.1k
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Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 2 days ago by ★ 4.8k • written 24 days ago by • 0
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How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2 RUVSeq
5 days ago Simran • 0
1
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4
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360
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DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
10 days ago • updated 5 days ago Lennie • 0
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4
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443
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 12 days ago by • 0
1
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1
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766
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Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
updated 15 days ago by 68k • written 15 days ago by • 0
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2
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1.2k
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
18 days ago • updated 17 days ago Luca • 0
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2
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414
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Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 12 days ago by 43k • written 21 days ago by ▴ 20
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1
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192
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DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 23 days ago by 43k • written 24 days ago by • 0
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3
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616
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how many significant figures are there in DESeq2 output
DESeq2
updated 28 days ago by ★ 4.8k • written 29 days ago by ▴ 180
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5
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1.0k
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Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
4 weeks ago picasa1983 • 0
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7
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2.0k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 4 weeks ago by ▴ 10 • written 6.0 years ago by ▴ 20
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1
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349
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How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differential Gene Expression analysis in scRNA-seq?
SingleCellData DESeq2 pseudobulk sing
updated 4 weeks ago by 68k • written 4 weeks ago by • 0
1
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1
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466
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Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 4 weeks ago by ★ 1.4k • written 4 weeks ago by ▴ 10
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1
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298
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DEseq2 design for additive treatment
DESeq2
updated 4 weeks ago by ★ 4.8k • written 4 weeks ago by • 0
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2
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549
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Plot title for PCA in DESeq2
DESeq2
5 weeks ago • updated 4 weeks ago AL • 0
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3
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570
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 5 weeks ago by 43k • written 5 weeks ago by • 0
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2
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1.1k
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 6 weeks ago by ★ 4.8k • written 6 weeks ago by • 0
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1
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162
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 6 weeks ago by 43k • written 7 weeks ago by • 0
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3
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530
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DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 6 weeks ago by • 0 • written 7 weeks ago by • 0
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2
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388
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accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 7 weeks ago by • 0 • written 7 weeks ago by • 0
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3
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452
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displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 4 weeks ago by • 0 • written 7 weeks ago by • 0
0
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3
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424
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 7 weeks ago by • 0 • written 9 weeks ago by ▴ 10
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1
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237
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 8 weeks ago by 43k • written 8 weeks ago by • 0
2
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2
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476
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 8 weeks ago by ★ 1.4k • written 9 weeks ago by • 0
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4
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986
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Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
9 weeks ago • updated 8 weeks ago Quang NN ▴ 10
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2
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603
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How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
9 weeks ago Blandine • 0
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5
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377
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 9 weeks ago by • 0
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4
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551
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
9 weeks ago Quang NN ▴ 10
2
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5
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449
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Differential variability modelling with vst() expression
limma DESeq2
written 11 weeks ago by • 0
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3
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577
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 11 weeks ago by • 0
2
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9
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1.1k
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
11 weeks ago • updated 9 weeks ago Quang NN ▴ 10
1
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1
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469
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 11 weeks ago by 43k • written 11 weeks ago by • 0
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1
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223
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 11 weeks ago by ★ 1.4k • written 11 weeks ago by • 0
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1
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421
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Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 12 weeks ago by 43k • written 3 months ago by • 0
2
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1
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426
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Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 12 weeks ago by 43k • written 3 months ago by • 0
0
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2
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418
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
3 months ago • updated 12 weeks ago Kucsera • 0
1
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1
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436
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
1
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9
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982
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 3 months ago by ▴ 30
4
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2
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556
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 3 months ago by ★ 4.8k • written 3 months ago by ▴ 10
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5
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686
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Deseq2 Design
RNASeq DESeq2
updated 3 months ago by 68k • written 3 months ago by • 0
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5
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704
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p value is 0, padj is 0
DESeq2
3 months ago Wirayatida • 0
1
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2
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677
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
3 months ago georgii.vdovin • 0
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7
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1.0k
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 3 months ago by • 0 • written 3 months ago by • 0
0
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1
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385
views
Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 3 months ago by 43k • written 3 months ago by ▴ 20
0
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3
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526
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DESeq2 - Comparing Comparisons
DESeq2
updated 3 months ago by 68k • written 3 months ago by • 0
0
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4
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654
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lfcShrink and alpha value
lfcShrink DESeq2
4 months ago • updated 3 months ago cropero • 0
2
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1
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425
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 3 months ago by 43k • written 4 months ago by • 0
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2
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300
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
0
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2
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337
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
4 months ago Anna • 0
50 results • Page 1 of 1
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Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran by Aaron Lun ★ 28k
It's calling C++ code, see the relevant function definitions on [GitHub](https://github.com/knncolle/BiocNeighbors/blob/master/src/generics…
Answer: DESeq2 by ATpoint ★ 4.8k
Time courses are often inevitable batches but you should have done the library prep at the same day, just extract RNA per day. If not then …
Comment: Package developing and interoperation with Bioconductor by slizchap • 0
Thank you so much for your answer. This was very useful, I will optimize my functions so they can handle SE objects.
Comment: Package developing and interoperation with Bioconductor by slizchap • 0
Thank you so much for your answer, very useful!
Comment: Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files by Mike Smith ★ 6.6k
Tricky to try and debug this without some example files to work with. Can you provide the output of `traceback()` called immediately after…
Votes
Is it possible to speed up VariantAnnotation's rowRanges function when converting to a dataframe?
Answer: Is it possible to speed up VariantAnnotation's rowRanges function when convertin
Comment: ComBat with repeated measures
Answer: Package developing and interoperation with Bioconductor
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
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