Showing : deseq • reset
5
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Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 10
0
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3
replies
1.5k
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DESeq2 group comparison
deseq2 deseq differential binding analysis
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 60
3
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5
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1.7k
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Help with multi-factor Deseq analysis
deseq2 rnaseq deseq
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
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7
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1.7k
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Deseq 2 multiple comparisons (3 groups, 24 samples)
deseq
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
4
votes
1
reply
14k
views
The latest version of R is 3.5.1 and it is not compatible with many Bioconductor packages.
R deseq tcgabiolinks
7.1 years ago ansari.sarabio • 0
1
vote
5
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1.5k
views
Group Specific Condition Query
deseq2 deseq batcheffect
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 10
3
votes
7
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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
7.1 years ago blastzone.heimerdinger ▴ 20
0
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8
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2.7k
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DESeq2 Multi factor, multi time point comparison design formula
rna-seq deseq2 deseq R
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
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1
reply
883
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how to start normalization
deseq
7.2 years ago raghavaraghava049 • 0
0
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1
reply
1.2k
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Basemean always multiples of 0.5 in deseq2 results
deseq results baseMean
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
0
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3
replies
1.2k
views
3x2 comparisons in DEseq - time (3 time points) and two treatments
deseq2 deseq rna-seq multiple comparisons
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 60
2
votes
3
replies
1.8k
views
ASE using DESeq2
deseq2 deseq normalization allele specific expression rnaseq
updated 7.3 years ago by ★ 3.8k • written 7.3 years ago by • 0
0
votes
5
replies
1.7k
views
How to simulate time course RNA seq data using DESeq?
deseq2 R makeexampledeseqdataset deseq
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
3
votes
7
replies
3.2k
views
novice: building gene co-expression network using RNA-Seq data
rna-seq WGCNA deseq method coexpression
updated 7.4 years ago by ★ 3.0k • written 7.4 years ago by ▴ 10
1
vote
2
replies
2.0k
views
Deseq2 with replicate mean and variance information
deseq2 deseq differential analysis proteomics
7.5 years ago blehtine • 0
1
vote
8
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2.6k
views
DESeq2 : group specific effect of a treatment while controlling for individual effect
deseq2 DESeq design and contrast matrix deseq
7.5 years ago SPbeginner • 0
1
vote
3
replies
1.3k
views
DEseq2 sample imbalance
deseq
7.6 years ago • updated 7.5 years ago aishu.jp ▴ 30
0
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4
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14k
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Normalization by DEseq
Genetics Normalization DESeq Genetics Normalization DESeq
updated 7.6 years ago by • 0 • written 14.9 years ago by ▴ 20
0
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8
replies
6.5k
views
Comparing between two differential expression analysis - two different fold changes
Deseq deseq2 differential gene expression rnaseq statistical test
7.6 years ago Marina ▴ 40
0
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4
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1.7k
views
Normalise counts when tumour samples have normal tissue contamination.
deseq2 deseq edgeR rnaseq htseqcounts
7.6 years ago Deepali • 0
0
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2
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4.2k
views
Problem loading or running DESeq2
deseq could not find function
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
8
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3
replies
5.9k
views
DESeq2 with interaction using SVA
deseq2 sva interaction term grouping variable deseq
7.6 years ago kevin.kingsland ▴ 70
4
votes
6
replies
2.1k
views
DESeq2 design and stats question
deseq2 differential binding analysis deseq atac-seq
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 60
2
votes
10
replies
4.5k
views
DESeq2 results export padj sorted
deseq2 deseq differential binding analysis
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 60
2
votes
4
replies
2.7k
views
Matrix not full rank - DESeq2
deseq2 model matrix not full rank model.matrix deseq differential binding analysis
updated 7.7 years ago by ★ 3.8k • written 7.7 years ago by ▴ 60
2
votes
5
replies
1.7k
views
Mapping DESeq2 output back to chromosomal positions
deseq2 deseq diffbind differential binding analysis
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 60
41
votes
44
replies
13k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR p-value DESeq RNA-Seq
updated 7.8 years ago by ▴ 60 • written 8.4 years ago by ▴ 10
1
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2
replies
1.3k
views
DESeq possible when only rlog table available? (DESeq2 package)
deseq2 rlog deseq
7.8 years ago sreibe • 0
9
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17
replies
2.5k
views
DESeq2 design subcategories
deseq2 deseq differential binding analysis
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 60
2
votes
6
replies
2.9k
views
DESeq: Question about contrast and group-wise subsetting.
deseq2 deseq
7.8 years ago Bioinformatician_R ▴ 20
0
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1
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1.7k
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RNAseq _generating tx2gene table and using kallisto output to run DEseq
deseq annotate
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
4
votes
7
replies
2.0k
views
Filtering DESeq2 result export along multiple lines
deseq2 differential binding analysis deseq
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 60
1
vote
2
replies
1.0k
views
Appropriate DESeq2 design for multi-factor comparison within group?
deseq2 deseq
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 20
0
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4
replies
2.8k
views
Adaptation of DESeq/edgeR model for CRISPR drop-out screen
crispr edger deseq deseq2
updated 7.9 years ago by ★ 29k • written 7.9 years ago by • 0
2
votes
1
reply
1.4k
views
Receiving error trying to import matrix into DESeq2
deseq2 deseq differential binding analysis
updated 7.9 years ago by ▴ 60 • written 7.9 years ago by ▴ 60
0
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4
replies
4.9k
views
DESeq failure after update: unable to find an inherited method for function mcols for signature Rle
deseq2 deseq r version compatibility
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
0
votes
9
replies
6.4k
views
DESeq2 unequal sample sizes
deseq2 deseq sample size
7.9 years ago MrHodor • 0
6
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3
replies
4.7k
views
Add new columns to DESeqResults from text file by matching rownames.
deseq2 deseq merge data frames cbind s4vectors
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 20
1
vote
4
replies
24k
views
Adjusting for covariates in paired sample design DESeq2
deseq2 deseq paired samples covariates multiple time points
8.0 years ago imb ▴ 10
10
votes
14
replies
5.7k
views
Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma edger deseq deseq2
updated 8.0 years ago by 53k • written 8.0 years ago by ▴ 90
0
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8
replies
4.7k
views
DESeq2 for multiple comparisons over time
deseq multiple factor design
8.1 years ago ucheuna • 0
1
vote
1
reply
4.3k
views
Linear regression in DESeq2
deseq
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
3
votes
11
replies
4.3k
views
DESeq function taking too long
deseq2 deseq factor rnaseq
updated 8.2 years ago by ★ 3.0k • written 8.2 years ago by ▴ 30
0
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1
reply
1.4k
views
name of column in R
software error deseq metarnaseq HTSFilter columns
updated 8.2 years ago by ★ 13k • written 8.2 years ago by • 0
27
votes
22
replies
22k
views
DESeq2 for ChIP-seq differential peaks
deseq2 deseq chipseq
updated 8.2 years ago by ▴ 120 • written 10.0 years ago by ▴ 200
4
votes
3
replies
3.1k
views
Why does Deseq, Deseq2, and EdgeR give vastly different results.
edger deseq deseq2
8.3 years ago michael.steffen ▴ 20
7
votes
12
replies
9.8k
views
Confused in the usage of formula in DESeq or DESeq2
deseq2 deseq
updated 8.3 years ago by ▴ 60 • written 10.9 years ago by ▴ 20
1
vote
8
replies
1.9k
views
DESeq2 - selective calculation of differential gene expression
deseq2 deseq
updated 8.3 years ago by 43k • written 8.3 years ago by • 0
0
votes
5
replies
2.7k
views
normalization factors for ChIP/RNA-IP-seq data
edgeR DESeq edgeR DESeq
updated 8.4 years ago by • 0 • written 13.7 years ago by ▴ 370
5
votes
13
replies
7.4k
views
P values from Deseq Analysis
deseq
8.4 years ago Shrikant Pawar • 0
512 results • Page 2 of 11
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Comment: GO.db and others package Download failure by James W. MacDonald 68k
Also, you never need to use anything but `BiocManager::install` to install any package, which has the beneficial side effect of ensuring th…
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Yes. Your packages have odd Y version numbers (where the version is X.Y.Z). That means they are devel packages (release versions have even …
Comment: GO.db and others package Download failure by Skyler • 0
Am I using Bioc-devel?
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Is there a reason to use Bioc-devel? If not, you should be using the release version (which I am, and which installs `GO.db` without compla…
Comment: GO.db and others package Download failure by Skyler • 0
Hi James, Below I have inserted all of my code. I have run r as an administrator and not as an administrator. I have changed my CRANmirror …
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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