Showing : DESEQ2 • reset
3
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4
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2.6k
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Removing rows (countData) from a DESeq Object
DESeq2
4.7 years ago Bine ▴ 50
3
votes
1
reply
649
views
Using group instead of interaction term on a custom edited matrix
DESeq2
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
3
votes
5
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2.5k
views
Deseq2 Paired Samples Design
DESeq2
4.7 years ago • updated 4.6 years ago Rita • 0
1
vote
1
reply
1.4k
views
PCA rand heatmap of raw data
DESeq2 DiffSeq PrincipalComponent rlog heatmaps
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 30
2
votes
3
replies
1.4k
views
Single sided P-value for DESeq2 Likelihood Ratio Test
DESeq2 DESe
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
6
votes
11
replies
6.5k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 20 months ago by • 0 • written 4.7 years ago by ▴ 40
0
votes
2
replies
1.2k
views
Pair-wise DESeq2 using tximport (running time and multi-threading)
tximport DESeq2
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
1
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2
replies
3.8k
views
error in DESeq2 results(dds)
DESeq2 datasetfrommatrix results error
4.7 years ago james • 0
1
vote
4
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2.2k
views
goseq package loading issues
DESeq2 goseq
4.7 years ago avinashi • 0
1
vote
2
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3.2k
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Regarding transcripts to gene ID conversion in tximport
salmon tximport DESeq2
4.7 years ago Nikolay Ivanov • 0
0
votes
1
reply
1.1k
views
error during installation of 'DEseq2' package
DESeq2 Install
updated 4.7 years ago by 16k • written 4.7 years ago by • 0
2
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3
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2.1k
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DESeq2 extracting relevant contrasts with interactions
DESeq2 DifferentialExpression
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
1
vote
15
replies
12k
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Exporting DESeq2 filtered results
DESeq2
updated 2.1 years ago by 68k • written 4.7 years ago by ▴ 10
0
votes
3
replies
1.2k
views
deseq2 design with two variables
DESeq2
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 10
3
votes
4
replies
1.1k
views
Identifying differentially expressed genes
identifyingDifferentiallyexpressedgenes DESeq2
updated 4.7 years ago by ★ 5.0k • written 4.7 years ago by • 0
0
votes
3
replies
3.7k
views
why does stat column disappears after lfcshrink on deseq 2 and why does fgsea uses stat column (not affected by shrinking) for fgsea?
fgsea DESeq2
updated 4.8 years ago by ★ 5.0k • written 4.8 years ago by ▴ 30
2
votes
2
replies
1.9k
views
Gene Selection GTex for DESeq2 Analysis
DESeq2 GTEx
4.8 years ago Bine ▴ 50
1
vote
6
replies
1.2k
views
I can't get the 2 by 2 comparisons that I need because the matrix is not full of rank
DESeq2
updated 4.8 years ago by ★ 5.0k • written 4.8 years ago by • 0
1
vote
3
replies
1.7k
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
0
votes
7
replies
3.2k
views
Subtracting Background Signal Before DESeq Analysis
Salmon DESeq2
updated 4.5 years ago by 43k • written 4.8 years ago by ▴ 30
0
votes
3
replies
3.9k
views
How to setup a two factor design in DESeq2
DESeq2 two-factorialdesign
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 10
2
votes
2
replies
6.4k
views
Importing data into the DESeq2 pipeline using tximport
DESeq2 tximport
4.8 years ago Nikolay Ivanov • 0
4
votes
3
replies
1.6k
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2 phyloseq
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 10
0
votes
3
replies
917
views
Isolate two different condtitions from DeSeq2 object
SubsetConditions DESeq2
updated 4.7 years ago by 43k • written 4.8 years ago by • 0
1
vote
3
replies
1.7k
views
Unable to reproduce Pasilla dataset which fresh instalation
tutorial DESeq2 pasilla
4.8 years ago Carina • 0
0
votes
1
reply
930
views
Linear Regression Diagnostic Plots with DESeq2
DESeq2
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
0
votes
2
replies
4.6k
views
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘plotPCA’ for signature ‘"prcomp"’
plotGrouper DESeq2 plot
updated 4.8 years ago by ★ 5.0k • written 4.8 years ago by • 0
0
votes
1
reply
1.7k
views
Plotting the most expressed genes after conducting DESeq2
DESeq2 pheatmap apeglm
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 10
1
vote
1
reply
851
views
Analysis design for DESeq2
DifferentialExpression DESeq2
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
1
vote
2
replies
1.5k
views
How to get the dispersion values before fitting?
DESeq2
4.8 years ago raya.fai ▴ 60
3
votes
4
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3.7k
views
R Error: package ‘GenomeInfoDb’ could not be loaded on MacBook
error mac DESeq2 GenomeInfoDb R
4.9 years ago • updated 4.8 years ago Dan ▴ 20
6
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5
replies
1.7k
views
perform DESeq2 based on paired sample
DESeq2
4.8 years ago xiaofeiwang18266 ▴ 60
4
votes
4
replies
1.6k
views
DEseq2: working with unbalanced number of sample in tumor study?
Deseq2 RNASeqRData unbalancedsamplesize
updated 3.5 years ago by 43k • written 4.8 years ago by • 0
2
votes
2
replies
1.6k
views
DESeq2 in R
DESeq2 apeglm
updated 4.8 years ago by ★ 1.4k • written 4.8 years ago by ▴ 10
4
votes
9
replies
2.1k
views
Variance stabilising transformation to within given range
DESeq2 scaling vst
updated 4.8 years ago by ★ 13k • written 4.8 years ago by ▴ 60
1
vote
2
replies
643
views
DESeq2
DESeq2
4.8 years ago amoaristotle ▴ 10
1
vote
4
replies
1.4k
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DESeq2 Design formula matrix not full rank
DESeq2 matrixnotfullrank Designformula DEseq2
4.8 years ago Nicolò • 0
0
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2
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1.7k
views
DSEQ apeglm
DESeq2 apeglm
4.8 years ago amoaristotle ▴ 10
0
votes
5
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2.6k
views
ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2 ZINB zinbwave deseq
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
0
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4
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2.3k
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DEseq2: setting up the correct contrast.
DESeq2 RNASeq
updated 4.8 years ago by ★ 1.4k • written 4.8 years ago by • 0
2
votes
1
reply
1.8k
views
apeglm -- influence of reference level on logFC and svalues
DESeq2 apeglm
updated 4.8 years ago by 43k • written 4.8 years ago by ★ 5.0k
1
vote
5
replies
2.8k
views
How can I use bioconductor and Deseq2 in linux ubuntu 18
RiboProfiling DESeq2 Bioconductor RNASeqRData
updated 3.1 years ago by ★ 4.0k • written 4.8 years ago by • 0
3
votes
3
replies
2.6k
views
Normalisation in DESeq2
DESeq2
updated 4.8 years ago by ★ 5.0k • written 4.8 years ago by ▴ 50
1
vote
1
reply
1.3k
views
No result from plotPCA()
DESeq2 RNASeq plotpca
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
2
votes
4
replies
2.5k
views
DESeq2 results change dramatically after scaling + centering of numeric variable
DESeq2
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by ▴ 20
2
votes
6
replies
1.5k
views
DESeq2 anormally high estimation of Log2FoldChange
DESeq2
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
2
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3
replies
1.6k
views
Independent filtering of NGS data
independentfiltering DESeq2 CRISPR
4.8 years ago Rubén • 0
2
votes
3
replies
2.7k
views
Gene Ontology Analysis of DE Genes
clusterProfiler AnnotationDbi OrgDb goseq
updated 4.8 years ago by 68k • written 4.8 years ago by ▴ 30
3
votes
3
replies
1.6k
views
DESeq2 for time-course with nested individuals
DESeq2
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 10
2
votes
3
replies
1.5k
views
DeSEQ2 factor effect without interaction effect
DESeq2 Interactions
4.8 years ago cossardg ▴ 10
4,839 results • Page 32 of 97
Recent ...
Replies
Answer: Create consensusMatrix for codon bases by Kevin Blighe ★ 4.0k
To address your query on generating a codon frequency matrix analogous to the output from `consensusMatrix` for a `DNAStringSet` object, no…
Answer: Finding duplicated entries in GRangesList by Kevin Blighe ★ 4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: sigDF object in sesame by Kevin Blighe ★ 4.0k
Your interpretation of the column headers in the SigDF object is correct: MG corresponds to the methylated signal intensity in the green ch…
Answer: DESeq2 on non-RNASeq counts data by Kevin Blighe ★ 4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hello Rui Tang, The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Votes
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
Answer: Identifying differentially expressed genes in individual samples from a large co
Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
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