Showing : deseq • reset
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evaluate the variable importance on genes
DESeq2 deseq
12 weeks ago Meme • 0
0
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2
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353
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Running DESeq on normalized data
deseq DESeq2
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
2
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2
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546
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Predicting missing values splines DESeq2
deseq DESeq2
6 months ago georgii.vdovin • 0
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1
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401
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Controling for Covariates With a Continuous Predictor Variable
Deseq DESeq2
updated 6 months ago by 42k • written 6 months ago by • 0
0
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1
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685
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Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 8 months ago by 66k • written 8 months ago by • 0
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3
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994
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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
0
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4
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675
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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 10 months ago by 42k • written 10 months ago by ▴ 20
1
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636
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summarizeToGene in tximeta causing vastly different results
DESeq2 deseq txime tximeta
updated 13 months ago by 42k • written 13 months ago by • 0
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4
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1.3k
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Volcano plot becomes flipped when I add a third condition
DESeq2 volcanoplot deseq HELP contrast
updated 15 months ago by ▴ 780 • written 15 months ago by • 0
0
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1
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578
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What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 16 months ago by 42k • written 16 months ago by ▴ 10
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1
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755
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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 16 months ago by ★ 1.5k • written 16 months ago by ▴ 10
1
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1
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534
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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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947
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DESeq2 is renaming gene names and lack of downregulated genes
DESeq DESeq2
22 months ago manwar • 0
1
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1
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796
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Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 23 months ago by 42k • written 23 months ago by • 0
1
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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 2.0 years ago by ★ 1.4k • written 2.0 years ago by ▴ 10
1
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5
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1.5k
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Potential outlier/high variance
deseq DESeq2
updated 2.1 years ago by 42k • written 2.1 years ago by • 0
1
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2
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934
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Deseq2 with imbalanced design
Deseq
2.2 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 42k • 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 2.6 years ago by 42k • written 2.6 years ago by • 0
4
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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
2
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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 jbnrodriguez ▴ 10
1
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2
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1000
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DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq DESeq
2.7 years ago krawczyk.margarita • 0
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 2.8 years ago by 42k • written 2.8 years ago by • 0
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
3.0 years ago ayy2110 • 0
0
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3
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2.3k
views
Understanding MA plot distortion
DESeq2 MAplot deseq
updated 3.2 years ago by 42k • written 3.2 years ago by • 0
1
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2
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968
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metage problem with DESeq
DESeq metagene2 metagene
updated 3.2 years ago by ▴ 10 • written 3.2 years ago by ▴ 10
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5
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1.8k
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ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2 ZINB zinbwave deseq
updated 3.3 years ago by 42k • written 3.3 years ago by • 0
1
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2
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995
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DESeq Error (nbinomTest ())
Deseq nbinomTest
4.0 years ago canfield ▴ 10
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7
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1.9k
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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 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 0
2
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5
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5.7k
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ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’ DESeq
written 4.1 years ago by ▴ 10
2
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2
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878
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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 42k • 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 4.2 years ago by ★ 3.7k • written 4.2 years ago by • 0
0
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7
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1.2k
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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
0
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1
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1.3k
views
DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 4.5 years ago by 42k • written 4.5 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 4.5 years ago by 42k • written 4.5 years ago by ▴ 180
1
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2
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912
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Filtering extraneous samples affects DESeq results. What is going on?
deseq deseq2
updated 4.8 years ago by 42k • written 4.8 years ago by • 0
4
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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 4.8 years ago by ▴ 40 • written 4.8 years ago by • 0
0
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0
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959
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Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
4.9 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 5.5 years ago by 42k • written 5.5 years ago by ▴ 10
0
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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 42k • written 5.5 years ago by • 0
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 42k • 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 42k • written 5.6 years ago by ▴ 10
0
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3
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1.1k
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DESeq2 group comparison
deseq2 deseq differential binding analysis
updated 5.7 years ago by 42k • written 5.7 years ago by ▴ 60
3
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5
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1.3k
views
Help with multi-factor Deseq analysis
deseq2 rnaseq deseq
updated 5.7 years ago by 42k • written 5.7 years ago by • 0
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Thank you so much!
Answer: recount3 problem downloading data from source sra by Leonardo Collado Torres ★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman by minardsmitha ▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Answer: Documenting resources in an `ExperimentHub` package? by James W. MacDonald 66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue by shepherl 3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Votes
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Comment: Ensembl plants at annotationHub?
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
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Scholar to Mike Smith ★ 6.5k
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