Showing : DESeq2 • reset
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DESeq2 filtering vs edgeR filtering
DESeq2
5 weeks ago • updated 23 days ago fr8712ca-s • 0
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DEG with low counts
DESeq2
updated 2 hours ago by 41k • written 4 days ago by • 0
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 2 hours ago by 41k • written 4.6 years ago by ▴ 10
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 23 hours ago by • 0 • written 8.8 years ago by ▴ 30
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
28 days ago • updated 22 days ago Chanderkant Chaudhary • 0
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How to retrieve detailed regression results from deseq2
DESeq2
updated 4 days ago by 41k • written 8 days ago by ▴ 10
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 1 day ago by ★ 4.0k • written 2 days ago by • 0
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2
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
29 days ago • updated 28 days ago kcarey • 0
2
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4
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DESeq2 setting significant p-value
DESeq2
updated 3 minutes ago by • 0 • written 5.0 years ago by ▴ 10
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3
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DESeq filtering specific to contrasts
DESeq2
updated 2 hours ago by 41k • written 9 weeks ago by • 0
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73
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covariate with negative and positive values
DESeq2
updated 22 hours ago by 41k • written 2 days ago by • 0
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2
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179
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 9 days ago by 41k • written 14 days ago by ▴ 30
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128
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
16 days ago Layal • 0
1
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6
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392
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 15 days ago by 41k • written 15 days ago by • 0
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54
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 22 hours ago by 41k • written 1 day ago by • 0
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 22 hours ago by 41k • written 1 day ago by • 0
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48
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rlog transformation
DESeq2
updated 22 hours ago by 41k • written 1 day ago by • 0
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1
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147
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collapseReplicates dimension error
DESeq2 Dese
updated 24 days ago by 41k • written 28 days ago by • 0
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1
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145
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DESeq2 - Missing values in count matrix
DESeq2
updated 14 days ago by 65k • written 14 days ago by • 0
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2
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214
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Regressing out batch effects
DESeq2
updated 9 days ago by 41k • written 14 days ago by • 0
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5
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1.1k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 2 days ago by • 0 • written 10 months ago by • 0
3
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2
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189
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
25 days ago • updated 24 days ago Anita ▴ 10
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1.2k
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DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 18 days ago by ★ 13k • written 9 months ago by ▴ 10
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3
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PCA of different bacterial species
DESeq2
updated 23 days ago by 41k • written 23 days ago by ▴ 10
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4
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553
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 2 days ago by 41k • written 5 months ago by • 0
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2
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132
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 14 days ago by 65k • written 14 days ago by • 0
0
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1
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132
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 21 days ago by 41k • written 21 days ago by • 0
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1
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109
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Bioinformatics student
Des DESeq2
updated 6 days ago by • 0 • written 6 days ago by • 0
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3
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140
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 3 days ago by 41k • written 3 days ago by ▴ 20
2
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3
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271
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DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 29 days ago by 41k • written 4 weeks ago by ▴ 20
1
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2
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153
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Design Matrix within group comparison more than two groups
DESeq2
6 days ago hemantcnaik • 0
0
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1
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129
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 9 days ago by 41k • written 9 days ago by • 0
0
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4
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215
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 16 days ago by 41k • written 17 days ago by • 0
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2
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142
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
17 days ago • updated 16 days ago michelafrancesconi8 • 0
0
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3
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100
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
updated 6 hours ago by ★ 4.0k • written 1 day ago by • 0
0
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1
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94
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Deseq2 Rlog transformation
DESeq2
updated 4 days ago by ★ 4.0k • written 5 days ago by • 0
0
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1
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141
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DESeq2 gives an error and R crashes
DESeq2
8 days ago • updated 7 days ago Shefali • 0
37 results • Page 1 of 1
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Comment: DESeq2 setting significant p-value by Dev • 0
Sir but when I put in the data via the csv file, it was showing the gene names then but now when i set it in the form factor it is not show…
Answer: OrgDb for maize by James W. MacDonald 65k
``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% snapshotDate(): 2023-10-23 > query(hu…
Comment: Which input file is used for DGEList in EgdeR? by i.atanasoai • 0
Understood, Thank you very much for the reply, very kind.
Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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