Showing : Deseq • reset
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Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 10
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DESeq2 group comparison
deseq2 deseq differential binding analysis
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 60
3
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5
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Help with multi-factor Deseq analysis
deseq2 rnaseq deseq
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
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Deseq 2 multiple comparisons (3 groups, 24 samples)
deseq
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
4
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The latest version of R is 3.5.1 and it is not compatible with many Bioconductor packages.
R deseq tcgabiolinks
7.3 years ago ansari.sarabio • 0
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Group Specific Condition Query
deseq2 deseq batcheffect
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
3
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1.6k
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The discrepancy between the mean of extracted fitted value and calculated mean and SE based on LFC.
deseq2 deseq
7.3 years ago blastzone.heimerdinger ▴ 20
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DESeq2 Multi factor, multi time point comparison design formula
rna-seq deseq2 deseq R
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
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reply
915
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how to start normalization
deseq
7.4 years ago raghavaraghava049 • 0
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Basemean always multiples of 0.5 in deseq2 results
deseq results baseMean
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
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3
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3x2 comparisons in DEseq - time (3 time points) and two treatments
deseq2 deseq rna-seq multiple comparisons
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 60
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3
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1.8k
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ASE using DESeq2
deseq2 deseq normalization allele specific expression rnaseq
updated 7.5 years ago by ★ 3.8k • written 7.5 years ago by • 0
0
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5
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How to simulate time course RNA seq data using DESeq?
deseq2 R makeexampledeseqdataset deseq
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
3
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7
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novice: building gene co-expression network using RNA-Seq data
rna-seq WGCNA deseq method coexpression
updated 7.6 years ago by ★ 3.0k • written 7.6 years ago by ▴ 10
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2
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Deseq2 with replicate mean and variance information
deseq2 deseq differential analysis proteomics
7.7 years ago blehtine • 0
1
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8
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2.7k
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DESeq2 : group specific effect of a treatment while controlling for individual effect
deseq2 DESeq design and contrast matrix deseq
7.8 years ago • updated 7.7 years ago SPbeginner • 0
1
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DEseq2 sample imbalance
deseq
7.8 years ago • updated 7.7 years ago aishu.jp ▴ 30
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4
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14k
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Normalization by DEseq
Genetics Normalization DESeq Genetics Normalization DESeq
updated 7.8 years ago by • 0 • written 15.1 years ago by ▴ 20
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8
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Comparing between two differential expression analysis - two different fold changes
Deseq deseq2 differential gene expression rnaseq statistical test
7.8 years ago Marina ▴ 40
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Normalise counts when tumour samples have normal tissue contamination.
deseq2 deseq edgeR rnaseq htseqcounts
7.8 years ago Deepali • 0
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Problem loading or running DESeq2
deseq could not find function
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
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3
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DESeq2 with interaction using SVA
deseq2 sva interaction term grouping variable deseq
7.9 years ago kevin.kingsland ▴ 70
4
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2.2k
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DESeq2 design and stats question
deseq2 differential binding analysis deseq atac-seq
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 60
2
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10
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4.6k
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DESeq2 results export padj sorted
deseq2 deseq differential binding analysis
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 60
2
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4
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2.8k
views
Matrix not full rank - DESeq2
deseq2 model matrix not full rank model.matrix deseq differential binding analysis
updated 7.9 years ago by ★ 3.8k • written 7.9 years ago by ▴ 60
2
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5
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1.8k
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Mapping DESeq2 output back to chromosomal positions
deseq2 deseq diffbind differential binding analysis
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 60
41
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44
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14k
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Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR p-value DESeq RNA-Seq
updated 8.0 years ago by ▴ 60 • written 8.6 years ago by ▴ 10
1
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2
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1.4k
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DESeq possible when only rlog table available? (DESeq2 package)
deseq2 rlog deseq
8.0 years ago sreibe • 0
9
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17
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2.6k
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DESeq2 design subcategories
deseq2 deseq differential binding analysis
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 60
2
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6
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3.0k
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DESeq: Question about contrast and group-wise subsetting.
deseq2 deseq
8.0 years ago Bioinformatician_R ▴ 20
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1.7k
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RNAseq _generating tx2gene table and using kallisto output to run DEseq
deseq annotate
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
4
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7
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2.1k
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Filtering DESeq2 result export along multiple lines
deseq2 differential binding analysis deseq
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 60
1
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2
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1.1k
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Appropriate DESeq2 design for multi-factor comparison within group?
deseq2 deseq
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 20
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Adaptation of DESeq/edgeR model for CRISPR drop-out screen
crispr edger deseq deseq2
updated 8.1 years ago by ★ 29k • written 8.1 years ago by • 0
2
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1
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1.4k
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Receiving error trying to import matrix into DESeq2
deseq2 deseq differential binding analysis
updated 8.1 years ago by ▴ 60 • written 8.1 years ago by ▴ 60
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4
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DESeq failure after update: unable to find an inherited method for function mcols for signature Rle
deseq2 deseq r version compatibility
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
0
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9
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6.6k
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DESeq2 unequal sample sizes
deseq2 deseq sample size
8.2 years ago MrHodor • 0
6
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3
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4.8k
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Add new columns to DESeqResults from text file by matching rownames.
deseq2 deseq merge data frames cbind s4vectors
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 20
1
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4
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24k
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Adjusting for covariates in paired sample design DESeq2
deseq2 deseq paired samples covariates multiple time points
8.2 years ago imb ▴ 10
10
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14
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5.9k
views
Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma edger deseq deseq2
updated 8.2 years ago by 53k • written 8.2 years ago by ▴ 90
0
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8
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4.8k
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DESeq2 for multiple comparisons over time
deseq multiple factor design
8.4 years ago ucheuna • 0
1
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1
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4.3k
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Linear regression in DESeq2
deseq
updated 8.4 years ago by 43k • written 8.4 years ago by • 0
3
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11
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4.5k
views
DESeq function taking too long
deseq2 deseq factor rnaseq
updated 8.4 years ago by ★ 3.0k • written 8.4 years ago by ▴ 30
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1
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name of column in R
software error deseq metarnaseq HTSFilter columns
updated 8.4 years ago by ★ 13k • written 8.4 years ago by • 0
27
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22
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DESeq2 for ChIP-seq differential peaks
deseq2 deseq chipseq
updated 8.4 years ago by ▴ 120 • written 10.2 years ago by ▴ 200
4
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3
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Why does Deseq, Deseq2, and EdgeR give vastly different results.
edger deseq deseq2
8.5 years ago michael.steffen ▴ 20
7
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12
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9.9k
views
Confused in the usage of formula in DESeq or DESeq2
deseq2 deseq
updated 8.5 years ago by ▴ 60 • written 11.1 years ago by ▴ 20
1
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8
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2.0k
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DESeq2 - selective calculation of differential gene expression
deseq2 deseq
updated 8.5 years ago by 43k • written 8.5 years ago by • 0
0
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5
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2.8k
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normalization factors for ChIP/RNA-IP-seq data
edgeR DESeq edgeR DESeq
updated 8.6 years ago by • 0 • written 13.9 years ago by ▴ 370
5
votes
13
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7.6k
views
P values from Deseq Analysis
deseq
8.6 years ago Shrikant Pawar • 0
512 results • Page 2 of 11
Recent ...
Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
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Popular Question to James W. MacDonald 68k
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