Showing : DESEQ2 • reset
2
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17
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3.3k
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How to reduce the impact of one varaible in Deseq2 or edgeR for multivariate value analysis?
MultipleComparison edgeR DESeq2
written 3.7 years ago by • 0
2
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2
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2.8k
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Time series and interaction in DESeq2
DESeq2
3.6 years ago Francesco ▴ 10
0
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2
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2.4k
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DESeq2 Log2 fold change does not make sense given change in TPM
DESeq2 TPM Foldchange
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
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2
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2.0k
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DESeq2 comparisons with multiple experimental variables?
DESeq2
updated 3.6 years ago by ★ 1.4k • written 3.6 years ago by • 0
0
votes
1
reply
966
views
DeSeq2 timecourse analysis
RNAseqRData DeSeq2
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
1
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2
replies
1.3k
views
Setting up read count data for DESeq2 to create a dds object
DESeq2
updated 3.6 years ago by ★ 1.4k • written 3.6 years ago by • 0
1
vote
1
reply
975
views
mgcv not loading on an update
m1_arm deseq2
updated 3.6 years ago by 43k • written 3.6 years ago by ▴ 10
0
votes
1
reply
791
views
DESeq how to evaluate design fit
DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by ▴ 20
1
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4
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1.6k
views
lncRNA Differential Expression Analysis
DESeq2 limma RNASeqData
3.6 years ago sushimoto • 0
0
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1
reply
975
views
DEG for multiple comparisons
DESeq2
3.6 years ago rand.alkaissy • 0
0
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2
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1.3k
views
Subsetting DESEQ2 VST Microbiome Data
DESeq2 16S VST
3.6 years ago vollkorrn • 0
0
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5
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2.7k
views
DESeqDataSetFromMatrix Function Error
DESeq2 Bioconductor
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
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3
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1.3k
views
DEseq2 Analysis over multiple tissues and conditions only gives 16 coefficients
DESeq2 RNASeq
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
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2
replies
2.9k
views
DESeq2 counts distribution across both genes and samples
deseq2 rnaseq
updated 3.6 years ago by • 0 • written 9.2 years ago by ▴ 50
1
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1
reply
1.1k
views
DESeq2 With Ratios from Nascent RNA-seq (Conversion Rate from slamdunk)
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 30
0
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5
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17k
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Error:The design matrix has the same number of samples and coefficients to fit, so estimation of dispersion is not possible. Treating samples as …
deseq2
updated 3.7 years ago by • 0 • written 5.1 years ago by • 0
2
votes
2
replies
895
views
Salmon counts for a gene but it is not in my DESeq2 tables
DESeq2
3.7 years ago tomtom ▴ 10
15
votes
18
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5.1k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2 edgeR goana GO
updated 3.7 years ago by 53k • written 3.7 years ago by ▴ 60
0
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1
reply
1.1k
views
LRT test in DESeq2 decide on the level of comparisons
DESeq2 LRT Model
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
1
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8
replies
3.0k
views
lfcShrink MA plot comparison
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
3
votes
4
replies
2.5k
views
Large difference between naive log2 and rlog transformation of count data
DESeq2 Normalization rlog
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
0
votes
6
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1.7k
views
ScRNA sequencing data _Seurat_Object_DESEQ2_Analayis_DGE
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
6
votes
2
replies
972
views
The number of controls versus treatment in differential expression analysis
DESeq2 edgeR limma
updated 3.7 years ago by 53k • written 3.7 years ago by ▴ 30
4
votes
1
reply
3.7k
views
Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2 RNASeq RNASeqData
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 40
2
votes
4
replies
5.5k
views
Making contrasts for multiple treatment groups using DESeq2
DESeq2
updated 3.2 years ago by 43k • written 3.7 years ago by • 0
4
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4
replies
1.3k
views
Covariates to be included in DE model
DESeq2 limma
updated 2.8 years ago by 43k • written 3.7 years ago by • 0
0
votes
3
replies
1.6k
views
dealing with outliers (deseq2)
maxcooks outliers zero counts DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 10
2
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2
replies
1.2k
views
Confounding DE results with DESeq2
isoforms DESeq2
3.7 years ago arfranco ▴ 130
0
votes
1
reply
972
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Including covariates from bulkRNAseq deconvolution to look for differentially expressed genes
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
1
vote
1
reply
1.0k
views
Strange error while running DESeq() function.
DESeq2 RNASeq RNASeqData
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 40
4
votes
6
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13k
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How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2 RNASeq RNASeqData
3.7 years ago treebig44 ▴ 40
1
vote
3
replies
1.8k
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Identifying DEG between development stages
plant Transcriptomics DESeq2 r
updated 3.7 years ago by ▴ 780 • written 3.7 years ago by • 0
1
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4
replies
2.6k
views
Unable to run "library(DESeq2)" successfully
DESeq2
written 4.8 years ago by • 0
0
votes
1
reply
1.1k
views
DESeq2 TimeCourse with alpha and ihw and genes that change up to a certain timepoint
TimeCourse DESeq2 Manual
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 110
2
votes
2
replies
1.2k
views
Could use some advice on analyzing ranks of expressed genes in two conditions,
GeneExpression DESeq2 ExpressionData
updated 3.7 years ago by • 0 • written 3.7 years ago by ▴ 10
1
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4
replies
1.4k
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Using DESeq2 to analyze m6A read counts from Nanopore sequencing
DESeq2
3.7 years ago YC • 0
0
votes
4
replies
1.6k
views
DESeq2 pseudotime series design?
DESeq2 design
3.7 years ago jordi.planells • 0
0
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1
reply
844
views
Some warnings when downloading "DESeq2"
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
3
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3
replies
2.4k
views
Deseq2 normalization steps
deseq2 normalization
updated 3.7 years ago by 43k • written 6.5 years ago by • 0
1
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3
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1.3k
views
scale of mu in assays(dds)
DESeq2
3.7 years ago chase.mateusiak • 0
2
votes
5
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2.0k
views
DESeq2 with baseline correction for gene expression differences
DESeq2 edgeR Transcriptomics
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
2
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5
replies
4.1k
views
DESeq2 and high prefiltering cutoff
DESeq2 prefiltering
3.7 years ago Chris • 0
4
votes
7
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2.2k
views
DESeq2: Subset Results from 2-Factor Design
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 30
5
votes
5
replies
3.1k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
3.7 years ago • updated 3.6 years ago 9906201a ▴ 20
1
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1
reply
979
views
Result table pvalue and adjusted p value
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 50
0
votes
2
replies
947
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Differential expression in fixed windows
DESeq2 RNASeq
3.7 years ago anatmela • 0
1
vote
2
replies
12k
views
Error in SummarizedExperiment(assays = SimpleList(counts = countData)
DESeq2
3.7 years ago Hanan • 0
2
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1
reply
1.2k
views
DESeq2 handling of replicates
DESeq2 RNASeq limma
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
4
votes
3
replies
1.9k
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Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2 idep RNASeqData
updated 3.7 years ago by ★ 1.4k • written 3.7 years ago by ▴ 10
0
votes
5
replies
7.3k
views
DESeq2/Differential expression analysis without replicates
DESeq2 DEG
updated 3.2 years ago by • 0 • written 3.8 years ago by • 0
4,838 results • Page 23 of 97
Recent ...
Replies
Answer: mzR-Rcpp compiler version issue by Laurent Gatto 1.6k
There are two issues here. First, a warning about mzR, that you can safely ignore. It tells you that mzR was compiled using a different …
Comment: Identifying differentially expressed genes in individual samples from a large co by jamie.gearing ▴ 60
Great. Yes, something descriptive is probably good enough, even if the p-values themselves are not so rigorous. Thanks very much Gordon!
Comment: Co-occurrence Network Analysis between Algae and Bacteria by Stefano Mangiola ▴ 40
Just a placeholder, that we are extending `sccomp` to co-occurrence analyses. Yours could be a good use-case to test first. We will be in t…
Answer: DESeq2 design for haplotype MPRA by aimesd808 • 0
I appreciate you telling me about this. Now it's crystal plain to me. Publish this: https://support.bioconductor.org/p/9162649/
Answer: Extract snp information from genomic regions with biomaRt -> "oaries_snp" by Kevin Blighe ★ 4.0k
My sincere apologies that my colleagues had ignored your question. The error occurs because the "chromosomal_region" filter is not valid…
Votes
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
Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Comment: Error installing Seqinfo
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