Showing : deseq • reset
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evaluate the variable importance on genes
DESeq2 deseq
9 weeks ago Meme • 0
0
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2
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333
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Running DESeq on normalized data
deseq DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
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2
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517
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Predicting missing values splines DESeq2
deseq DESeq2
5 months ago georgii.vdovin • 0
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1
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378
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Controling for Covariates With a Continuous Predictor Variable
Deseq DESeq2
updated 5 months ago by 41k • written 5 months ago by • 0
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1
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646
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Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 7 months ago by 65k • written 7 months ago by • 0
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3
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877
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Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq DESeq2
updated 9 months ago by ★ 4.1k • written 9 months ago by ▴ 10
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4
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650
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lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2 apeglm DESeq ApeGLM Ashr
updated 9 months ago by 41k • written 9 months ago by ▴ 20
1
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609
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summarizeToGene in tximeta causing vastly different results
DESeq2 deseq txime tximeta
updated 12 months ago by 41k • written 12 months ago by • 0
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4
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1.2k
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Volcano plot becomes flipped when I add a third condition
DESeq2 volcanoplot deseq HELP contrast
updated 14 months ago by ▴ 780 • written 14 months ago by • 0
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1
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563
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What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 15 months ago by 41k • written 15 months ago by ▴ 10
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1
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721
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Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 15 months ago by ★ 1.5k • written 15 months ago by ▴ 10
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2
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1.2k
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suggestions/comments on DESeq transcript wise analysis
convert DESeq convert DESeq
written 12.2 years ago by ▴ 190
1
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1
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518
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How to design multifactor DESEQ2 formula?
DESEQ DESEQ2
updated 20 months ago by ★ 4.1k • written 20 months ago by • 0
3
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2
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920
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DESeq2 is renaming gene names and lack of downregulated genes
DESeq DESeq2
21 months ago manwar • 0
1
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1
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778
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Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 22 months ago by 41k • written 22 months ago by • 0
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5
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1.2k
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Error in DEseq
DEseq RNASeqData
updated 23 months ago by ★ 4.1k • written 23 months ago by • 0
2
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1
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1.5k
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Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 23 months ago by ★ 1.3k • written 23 months ago by ▴ 10
1
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5
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1.4k
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Potential outlier/high variance
deseq DESeq2
updated 2.0 years ago by 41k • written 2.1 years ago by • 0
1
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2
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906
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Deseq2 with imbalanced design
Deseq
2.1 years ago Alex • 0
1
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4
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1.6k
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Test if a gene is NOT differentially expressed in DESeq2?
DESeq2 deseq
updated 2.3 years ago by 41k • written 2.3 years ago by • 0
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2
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1.1k
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DESeqDataSet design issue
DESeq DESeq2
2.4 years ago matthew.valentine • 0
1
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1
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1.5k
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DESeq2 rows did not converge in beta, how to solve
DESeq DESeq2
updated 2.5 years ago by 41k • written 2.5 years ago by • 0
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6
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1.7k
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Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
2.6 years ago s-rhussien • 0
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2
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2.3k
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Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
2.7 years ago • updated 2.6 years ago jbnrodriguez ▴ 10
1
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2
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981
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DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq DESeq
2.7 years ago krawczyk.margarita • 0
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2
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1.5k
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same padj for all the genes after DEseq analysis
etLRT WALD edgeR DESEq
updated 2.7 years ago by 41k • written 2.7 years ago by • 0
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1
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1.1k
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Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
2.9 years ago ayy2110 • 0
1
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2
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937
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metage problem with DESeq
DESeq metagene2 metagene
updated 3.1 years ago by ▴ 10 • written 3.2 years ago by ▴ 10
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3
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2.2k
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Understanding MA plot distortion
DESeq2 MAplot deseq
updated 3.2 years ago by 41k • written 3.2 years ago by • 0
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5
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1.7k
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ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2 ZINB zinbwave deseq
updated 3.2 years ago by 41k • written 3.2 years ago by • 0
2
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12
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4.5k
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Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2 deseq
updated 3.5 years ago by 41k • written 9.0 years ago by • 0
1
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978
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DESeq Error (nbinomTest ())
Deseq nbinomTest
3.9 years ago canfield ▴ 10
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7
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1.8k
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DESeq error: Error in validityMethod(object) : nrow(design) == ncol(object) is not TRUE
deseq2 DESeq nrow == ncol is not TRUE
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by • 0
2
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5
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5.6k
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ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’ DESeq
written 4.0 years ago by ▴ 10
2
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2
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860
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Mocking data for understanding interactions in DESeq2
deseq2 deseq
updated 4.1 years ago by ★ 3.7k • written 4.1 years ago by • 0
3
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5
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2.1k
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How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
deseq rna-seq filtering DE deseq2
updated 4.1 years ago by 41k • written 4.1 years ago by ▴ 830
1
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9
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1.3k
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Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2 DESeq
updated 4.1 years ago by ★ 3.7k • written 4.1 years ago by • 0
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7
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1.1k
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how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2 deseq
4.3 years ago MANYA_BIOINFO • 0
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1
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1.2k
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DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 4.4 years ago by 41k • written 4.4 years ago by ▴ 10
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3
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1.4k
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 4.4 years ago by 41k • written 4.5 years ago by ▴ 180
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4
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4.5k
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TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2 deseq normalization
updated 4.7 years ago by ▴ 40 • written 4.8 years ago by • 0
1
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2
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887
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Filtering extraneous samples affects DESeq results. What is going on?
deseq deseq2
updated 4.8 years ago by 41k • written 4.8 years ago by • 0
0
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0
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937
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Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
4.8 years ago kentfung ▴ 20
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9
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2.0k
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NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
5.2 years ago ariel ▴ 20
3
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12
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1.6k
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Why did I get NA p-values in DESeq with continuous variable?
deseq2 p-value continuous deseq
5.2 years ago ariel ▴ 20
2
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3
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1.9k
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DESeq2 count outlier replacement from Cook's threshold
deseq2 deseq rnaseq outliers count outliers
updated 5.4 years ago by 41k • written 5.4 years ago by ▴ 10
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1
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1.0k
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Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 5.5 years ago by 41k • written 5.5 years ago by • 0
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3
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1.2k
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Strange lfcShrink plot when running DESeq2 workflow
DESeq2 rnaseq rna-seq deseq2 deseq
5.6 years ago Ben ▴ 50
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7
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3.9k
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DESeq2 install problem
deseq
updated 5.6 years ago by 41k • written 5.6 years ago by • 0
5
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7
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3.6k
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Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 5.6 years ago by 41k • written 5.6 years ago by ▴ 10
50 results • Page 1 of 1
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Answer: SGSeq: moving toward diffex from SGSeq analysis by Leonard Goldstein ▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy) by James W. MacDonald 65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Votes
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
Awards • All
Popular Question to Ian D. ▴ 70
Popular Question to junhui.li11 • 0
Scholar to James W. MacDonald 65k
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