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Showing top results for tag: deseq2 • reset
1
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107
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Using NumReads column of quants.genes.sf file to build DESeq2 input
R deseq2 rna-seq salmon
updated 16 hours ago by 20k • written 17 hours ago by ▴ 10
0
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1
reply
182
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Perform DESeq2 with One factor with three levels vs Two factor with two levels
DESeq2
updated 19 hours ago by • 0 • written 2 days ago by • 0
0
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0
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95
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PyDeseq2 - InvalidIndexError
python rna-seq pandas pydeseq2 deseq2
1 day ago by tmanjonas • 0
2
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6
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2.4k
views
Question: can not obtain DESeq2 results
RNA-Seq DESeq2
updated 2 days ago by ▴ 10 • written 4.3 years ago by ▴ 10
5
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3
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386
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Selecting DEGs for gene ontology using clusterprofiler and DESeq2
R DESeq2 RNAseq
3 days ago by a.basitkhan1990 ▴ 60
0
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0
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151
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immunedeconv for RNAseq data
meta-analysis rna-seq immunedeconv deseq2
8 days ago by a.stef.44 ▴ 10
0
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2
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243
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error in DESeq2 Determines differentially expressed features from count tables
DESeq2
updated 8 days ago by 20k • written 9 days ago by • 0
2
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2
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232
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Highly skewed distribution of differentially expressed (DE) genes
R RNAseq Deseq2
updated 9 days ago by 4.3k • written 9 days ago by • 0
0
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5
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367
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weird entry in EnhanceVolcano Volcano plot -RNAseq
DEseq2 RNAseq EnhancedVolcano
updated 13 days ago by 44k • written 14 days ago by • 0
2
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1
reply
157
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Can VST be called Log2 expression in a paper?
DESeq2
updated 15 days ago by 85k • written 15 days ago by • 0
9
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10
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511
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How to handle RNA seq data with unbalanced % rRNA by group?
fastqscreen rRNA DESeq2 RNAseq DGE
updated 10 days ago by 8.9k • written 17 days ago by ▴ 40
2
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2
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298
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Outlier after DEseq2 in meta-analysis
meta-analysis rna-seq outlier DESeq2
16 days ago by a.stef.44 ▴ 10
5
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4
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521
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Which Should Take Priority When Selecting DEGs: FDR or Log Fold Change?
DESeq2 logFC FDR DEGs edgeR
17 days ago by bioinfo1994 ▴ 20
0
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1
reply
262
views
DeSeq2 filter transcripts
DeSeq2 RNA-seq RNA
updated 21 days ago by 11k • written 21 days ago by • 0
1
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2
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339
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DESeq2: adjusted p-values become NA when sub-setting samples
R DEG RNA-seq DESeq2
updated 21 days ago by 146k • written 21 days ago by ▴ 190
2
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3
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370
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Error function vst in DESeq2
vst DESeq2
updated 23 days ago by ▴ 600 • written 24 days ago by • 0
1
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4
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396
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Poor dispersion fit in DESeq2
deseq2 RNA-seq edgeR limma
updated 5 weeks ago by 44k • written 5 weeks ago by ▴ 20
0
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9
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824
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How to approach DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
multifactor DESeq2
5 weeks ago by duplessisantzel • 0
3
votes
1
reply
392
views
High inconsistency between edgeR and DESeq2
log-ratio edgeR GLM DESeq2
updated 6 weeks ago by ★ 3.0k • written 6 weeks ago by ▴ 10
1
vote
1
reply
193
views
Overestimate of ATAC-seq differential peaks
MACS2 ATAC-seq DESeq2
updated 6 weeks ago by ★ 18k • written 6 weeks ago by • 0
5
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7
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1.1k
views
Differential expressed genes - much more DE genes for one factor in the additive model than the interaction model . What may be the reason?
DESeq2
6 weeks ago by Pei ▴ 220
1
vote
4
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447
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Getting a list of up- and downregulated genes using DESeq2
geneID DESeq2
updated 8 weeks ago by 101k • written 8 weeks ago by • 0
0
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2
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369
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Find DE in single cell RNA sequencing
DE DESeq2 scRNAseq analysis
8 weeks ago by kayah ▴ 20
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0
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218
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Normalising and splitting TCGA data into train and test sets
RNA-Seq vst DESeq2 TCGA
8 weeks ago by RajSehmbi • 0
0
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2
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293
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Weird correlation between RIP-seq replicates
RIP-seq transformation RNA-seq DESeq2
updated 8 weeks ago by ▴ 290 • written 8 weeks ago by • 0
0
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0
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187
views
How to use compareCluster ?
gsea RNA-seq clusterprofiler deseq2
updated 8 weeks ago by 44k • written 8 weeks ago by ▴ 10
0
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3
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452
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DEseq2 with different designs matrix
DEseq2
8 weeks ago by QX ▴ 60
0
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11
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883
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Differential gene expression
DESEq2 Differential gene expression
updated 8 weeks ago by ▴ 90 • written 9 weeks ago by • 0
0
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0
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283
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DESeq2 Install in Jupyter Notebook
deseq2 Jupyter
updated 8 weeks ago by 44k • written 9 weeks ago by • 0
0
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14
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1.2k
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DEseq2 on expected counts
DEseq2 Normalize raw-counts
updated 9 weeks ago by 88k • written 11 weeks ago by ▴ 10
5
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2
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326
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How to Handle Unbalanced RNA-seq Data (710 vs. 15 Samples) Using DESeq2?
R DESeq2 Unbalanced RNA-seq groups
updated 9 weeks ago by ★ 1.8k • written 9 weeks ago by ▴ 140
0
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1
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364
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Batch Effect Correction in RNA-seq Data Using SVA and DESeq2
SVA Batch DESeq2 RNA-seq
updated 9 weeks ago by 88k • written 10 weeks ago by ▴ 20
0
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1
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344
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DEseq2 interactions
Deseq2
updated 10 weeks ago by 44k • written 10 weeks ago by • 0
5
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8
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637
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p-value/adjusted p-vlaue cutoff
adjusted-pvalue p-value DESeq2 fgsea
updated 10 weeks ago by 27k • written 10 weeks ago by • 0
0
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5
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572
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Differential gene expression (aiming to create heatmap) for raw RNAseq count data from different publications - how to?
R DESeq2 Differential-expression
updated 10 weeks ago by ★ 2.1k • written 11 weeks ago by • 0
0
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6
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495
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Batch correction for RNA-seq using ComBat-seq for same group and batch
SVA ComBat_seq ComBat DESeq2 RNA-seq
11 weeks ago by botloggy ▴ 10
1
vote
1
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290
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Testing for specific genes of whole RNA Sequencing
R DESeq2 Sequencing RNA
updated 11 weeks ago by 85k • written 11 weeks ago by ▴ 20
3
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4
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406
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Need help with design/workflow please?
deseq2 batch workflow
11 weeks ago by BioinfGuru ★ 2.1k
4
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8
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592
views
Help in Log2 transform CPM count
R edgeR dge Deseq2
updated 11 weeks ago by 44k • written 11 weeks ago by ▴ 60
3
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11
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1.1k
views
6 follow
How to solve DESeq2 Error in checkFullRank(modelMatrix) cause by biological replicates information?
DESEq2 DESEq
updated 11 weeks ago by 14k • written 12 weeks ago by • 0
0
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2
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410
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How to Fix "Error in checkForExperimentalReplicates(object, modelMatrix) :"?
DESeqDataSetFromMatrix R colData DESeq2 RNA-Seq
11 weeks ago by thatolivebranch • 0
2
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1
reply
372
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DESeq2 analysis of a chromosome region
gene-expression RNA-seq DESeq2
updated 12 weeks ago by ★ 2.1k • written 12 weeks ago by • 0
1
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3
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350
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DEG with several conditions
R gene-expression DESeq2 RNA-Seq
updated 12 weeks ago by ★ 2.1k • written 12 weeks ago by • 0
0
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1
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205
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Genes of Interest in a Multi-Tissue Analysis
VST DGE DESeq2
updated 13 hours ago by • 0 • written 12 weeks ago by • 0
3
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5
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625
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DEGs vs WGCNA: What am I really looking at?
deseq2 RNA-seq deg wgcna
12 weeks ago by christiantd • 0
1
vote
12
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1.8k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq DESeq2 DNA-contamination
updated 3 months ago by 146k • written 9 months ago by ▴ 40
0
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2
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357
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Batch correction for protein data
proteomics DESeq2 batch-correction
9 weeks ago by 4732b159 • 0
3
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2
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408
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is that statistical correct to use DEseq2 for proteomics data
proteomics DEseq2
updated 3 months ago by 85k • written 3 months ago by ▴ 60
0
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1
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312
views
DESeq2 on a complex design
RNA-seq DESeq2
updated 3 months ago by ★ 2.1k • written 3 months ago by • 0
2
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3
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6.0k
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DESeq2 vst function error
DESeq2 RNA-Seq R normalization
updated 3 months ago by ★ 4.3k • written 4.2 years ago by ▴ 90
50 results • Page 1 of 1
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Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by ATpoint 85k
> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect? You cannot. It's pe…
Comment: Comparing GSEA mutant data to wild type by conmul • 0
Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
Comment: How to determine whether it is 10x data by king • 0
Thank you for your answer, it's very inspiring.
Comment: Inquiry about depth of coverage and copy number variation by Chen • 0
Thanks Pierre, I was actually thinking about the duplicate PCR reads and didn't explain it properly. I have found a post mentioning that qu…
Comment: Can a read be aligned more than once? by GenoMax 146k
Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could im…
Comment: Statistical test to be used for dataset by allingt • 0
The choice of test depends on the types of variables involved and the hypothesis you have. But most importantly on the question you want am…
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I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
Comment: Comparing GSEA mutant data to wild type by allingt • 0
What do you mean by "significant gene"? How did you perform GSEA and on how did you rank your genes for it? From guesswork I might initiall…
Comment: Genes of Interest in a Multi-Tissue Analysis by allingt • 0
The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applica…
Comment: WGCNA: Why are my brown, yellow, and other modules not visible in the gene dendr by allingt • 0
Did you perform blockwise module detection by any chance? Are your results object's contents sorted in blocks?
Comment: Why does WGCNA use weighted correlation instead of Pearson correlation? by allingt • 0
The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
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any idea, how can I display the labels Pre and POst on the top of the heatmap? I am looking at complexheatmap package as to how they displa…
Comment: How can I determine the p-value of genes within each identified module in WGCNA? by allingt • 0
What p-value do you mean? When and how did you calculate it?
Answer: What is a genomic range that would almost always get decent WGS coverage but is by i.sudbery 20k
What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.
Answer: Using NumReads column of quants.genes.sf file to build DESeq2 input by i.sudbery 20k
One of the improvements that the using the `salmon` -> `tximport` -> `DESeq2` pipeline, over just a `counts`->`DESeq2` pipeline is the abil…
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