Showing : DESeq2 • reset
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 13 months ago by 43k • written 13 months ago by • 0
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392
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 14 months ago by ★ 1.4k • written 14 months ago by • 0
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712
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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 14 months ago by 43k • written 14 months ago by • 0
2
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814
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Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 14 months ago by 43k • written 14 months ago by • 0
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2
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862
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
14 months ago Kucsera • 0
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624
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
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1.8k
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 14 months ago by ▴ 40
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2
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1.5k
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 14 months ago by ★ 5.0k • written 14 months ago by ▴ 10
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5
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1.2k
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Deseq2 Design
RNASeq DESeq2
updated 14 months ago by 68k • written 14 months ago by • 0
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1.4k
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p value is 0, padj is 0
DESeq2
14 months ago Wirayatida • 0
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2
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
14 months ago georgii.vdovin • 0
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7
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 14 months ago by • 0 • written 14 months ago by • 0
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621
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 15 months ago by 43k • written 15 months ago by ▴ 20
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DESeq2 - Comparing Comparisons
DESeq2
updated 14 months ago by 68k • written 15 months ago by • 0
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4
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1.1k
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lfcShrink and alpha value
lfcShrink DESeq2
15 months ago anon • 0
2
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1
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992
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 15 months ago by 43k • written 15 months ago by • 0
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558
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
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2
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587
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
15 months ago Anna • 0
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2
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885
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Deseq2 res Function
DESeq2
updated 15 months ago by 68k • written 15 months ago by ▴ 10
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4
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844
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
15 months ago NB • 0
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5
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895
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Identical samples after deseq2 batch effect removal
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
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647
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 15 months ago by 68k • written 15 months ago by • 0
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2
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567
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
15 months ago Denise • 0
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490
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eRNAs count
RNASeq DESeq2
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
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701
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DESeq2 rerun returns different results
DESeq2
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
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595
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 15 months ago by 43k • written 15 months ago by • 0
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770
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
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2
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1.4k
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Handling biological replicates in DESeq2
DESeq2
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
5
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3
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30k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 7.1 years ago by ▴ 30
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6
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1.8k
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 15 months ago by 43k • written 15 months ago by ▴ 10
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631
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 16 months ago by • 0
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5
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1.7k
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
16 months ago LuciaNhu • 0
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871
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Average expression of genes across replicates
DESeq2
updated 16 months ago by ★ 5.0k • written 16 months ago by • 0
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
16 months ago info ▴ 10
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2.8k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
updated 11 months ago by • 0 • written 16 months ago by • 0
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604
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Deseq to output continous sequencing data
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
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4
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1.6k
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Adjusted p-values become NA when sub-setting samples
DESeq2
16 months ago txema.heredia • 0
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3
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1.8k
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 16 months ago by • 0
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2
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1.2k
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 16 months ago by • 0
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527
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Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
2
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3
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1.4k
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Analysis of large RNA-Seq Datasets
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
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4
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1.2k
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DESeq2 - interactions when using factors concatenated into group
DESeq2
16 months ago boczniak767 ▴ 740
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422
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
16 months ago JY • 0
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517
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How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
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2
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564
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how to extract expression matrix post deseq2
DESeq2
written 16 months ago by • 0
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2
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579
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Using Normalized Counts in DESeq2
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
3
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749
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When running contrasts, does it use normalized read counts?
DESeq2
16 months ago Katherine ▴ 20
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464
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How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 16 months ago by ★ 1.4k • written 16 months ago by • 0
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
16 months ago Eva ▴ 30
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4
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1.6k
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Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 16 months ago by ★ 5.0k • written 17 months ago by • 0
4,851 results • Page 3 of 98
Recent ...
Replies
Answer: Unable to find ENTREZ IDs by James W. MacDonald 68k
Those are the 'symbols', and are a concatenation of LOC and the NCBI Gene ID (what used to be called an Entrez Gene ID). As an example:http…
Answer: Inconsistencies between accessor functions for TxDb databases with selected seql by a2a2hd42aa • 0
Technical inconsistencies in database accessors can disrupt your workflow, but finding a reliable source to download online mobile games sh…
Comment: Can sample-level weights be used when analysing GSVA scores in limma? by A.Barden ▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by a2a2hd42aa • 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Votes
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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