Showing : DESEQ2 • reset
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1.4k
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Deactivate svalue=T in lfcShrink - DESeq2 - apeglm
deseq2 apeglm
updated 6.6 years ago by 43k • written 6.6 years ago by ★ 5.0k
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4
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1.1k
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DESeq2: Minimal experiment-wide log-fold change differences between treatments
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
3
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5
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992
views
Differential Expression Analysis for Single Population RNASeq in Deseq2
deseq2 normalization
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
3
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3
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1.1k
views
Extracting within subject effect in a between and within subject model with DESeq2
deseq2 design
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 40
0
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3
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769
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Variance for paired design - DESeq2
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 30
6
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3
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2.8k
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Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
deseq2
updated 6.6 years ago by ▴ 10 • written 6.6 years ago by ▴ 20
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3
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2.5k
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DESeq2 log2FoldChange is very large and differs strongly from manually calculated.
deseq2 RNAseq
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 20
0
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3
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875
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DESeq2: Should lfcShrink require contrast or coef if a results object is supplied?
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
1
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1
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2.2k
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"degPatterns" showed 6 clusters, but why no genes in cluster 1-4, but all clustering genes in cluster 5 and 6
DEGreport deseq2
updated 6.6 years ago by ▴ 140 • written 6.6 years ago by ▴ 10
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4
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1.6k
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DESeq2 PCOA Plots
deseq2
6.6 years ago amgodogma ▴ 10
1
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5
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1.3k
views
Testing Interactions without an interaction term in the design formula
deseq2 interactions
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 30
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2
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1.5k
views
Error when creating a DESeqDataSet object
deseq2 DESeqDataSet
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 30
0
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7
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1.1k
views
Unexpected p-values by DESeq2
deseq2 normalization
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
1
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2
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1.1k
views
Two factors design with DESEq2
deseq2 genes expression
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
1
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1
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586
views
add gene names to rlog transformation for heatmap using the library "org.Hs.eg.db"
deseq2 annotation
updated 6.6 years ago by 68k • written 6.6 years ago by ▴ 10
2
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3
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3.9k
views
DESeq2- preliminary study no replicates
deseq2 replicates error DESeqDataSetFromMatrix
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
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2
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597
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Deseq2 giviing different results with Linux and Windows
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
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2
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919
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Do a subset of s4 object based on ensembl gene biotype?
deseq2
6.6 years ago mdahl3105 • 0
0
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10
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1.1k
views
DESeq help for comparing contrasts
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
0
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1
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572
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Adding samples data from different experiment
rna-seq deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 60
0
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3
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1.1k
views
Normalisation upstream rlog
deseq2 rlog
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
1
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1
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1.5k
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2 vst cox-regression Salmon Tximport
updated 6.6 years ago by 43k • written 6.7 years ago by • 0
1
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1
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737
views
DESeq Error: Duplicate rownames not allowed
deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
2
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3
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6.2k
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Pvalue equals 0 in DESeq2 & fixing for volcano plot
deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
1
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6
replies
2.2k
views
Zero pvalues after lfcShrink of DESeq2 package
deseq2 pvalue lfcshrink
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 10
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1
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1.7k
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DESeq2: error, the model matrix is not full rank, linear combinations
deseq2
updated 6.7 years ago by ★ 3.0k • written 6.7 years ago by • 0
0
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1
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2.2k
views
DESeq2 Exploratory analysis of a single timepoint vs control
DESeq2
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
0
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3
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1.6k
views
Is it possible to use DESeq2 likelihood ratio test for time-course analysis to analyse MNase-Seq data?
timecourse mnase-seq deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
0
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2
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1.4k
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DESeq2 testing ratio of ratios in a ribosomal profiling with batch
deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
0
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1
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1.1k
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Deseq2 Variance Stabalizing Transformation -- loss zeros to standard integer
deseq2 variancestabalizingtransformation vst
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
0
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2
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1.1k
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DESeq2 lfcThreshold question: different numbers when filtering in results() vs. filtering afterwards?
deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
1
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3
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2.3k
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DESeq2 for QuantSeq data
deseq2
updated 6.7 years ago by ▴ 20 • written 6.7 years ago by ▴ 20
2
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17
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3.8k
views
Computationally Singular Matrices - DESeq
deseq2 rnaseq sva
updated 3.1 years ago by 43k • written 6.7 years ago by • 0
0
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1
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509
views
DESeq2 excess of positive signals
deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
1
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3
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1.1k
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DESeq2 - Method-of-moments - negative binomial
deseq2 method-of-moments negative binomial
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 30
1
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2
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1.1k
views
using DESeq2 v 1.18 in Bioconductor v. 3.8
deseq2 bioconductor
updated 6.7 years ago by 4.2k • written 6.7 years ago by ▴ 10
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3
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1.2k
views
More significant genes with alpha 0.05 than 0.1 DESeq2
deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
0
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3
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1.4k
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model design in rna seq - deseq2
deseq2 rna-seq variability model-design
6.7 years ago acebolladaso.iacs • 0
3
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4
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1.6k
views
RNA-seq Statstical Models and Transcriptional Amplification
edgeR DESeq2 Transcriptional Amplification
updated 6.7 years ago by ★ 29k • written 6.7 years ago by ★ 1.6k
2
votes
5
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17k
views
Conversion from counts to FPKM
counts fpkm fpkm() normalization deseq2
updated 2.1 years ago by • 0 • written 6.9 years ago by • 0
1
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2
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990
views
Normalization method for Exosome small RNA-Seq (DESeq2)
deseq2
6.7 years ago IV ▴ 30
0
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1
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715
views
Applying external size factors to a dds did not yield expected results
DESeq2 normalization size factors
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 10
1
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1
reply
874
views
DESeq2 for 16S rRNA
deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
1
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3
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1.4k
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Deseq2 polysome profiling analysis
deseq2 rnaseq
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 10
1
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8
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1.6k
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DEseq2 time-series design
deseq2
updated 13 months ago by ▴ 10 • written 6.7 years ago by • 0
1
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3
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1.4k
views
Deseq2 PCA Anlysis
deseq2 pca
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
0
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2
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1.1k
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Problem in installing
software error deseq2
updated 6.7 years ago by 25k • written 6.7 years ago by ▴ 30
2
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4
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2.0k
views
What is the biological meaning of genes with FC = 0 after shrinkage
deseq2 apeglm
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
1
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12
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1.9k
views
DEseq2 : Difference between results and plotCounts
deseq2
6.7 years ago thomas.derrien • 0
0
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3
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1.4k
views
DESEQ2 Batch effect
deseq2 batch
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
4,839 results • Page 52 of 97
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Answer: Feedback needed on new user-friendly BED file tool by Kevin Blighe ★ 4.0k
Unsure, James, let me try to answer I use BED files frequently in my bioinformatics work, primarily through command-line tools like BEDT…
Answer: sigDF object in sesame by Kevin Blighe ★ 4.0k
The output you observe from the SigDF object is normal and corresponds to the methylated and unmethylated intensities, separated by color c…
Answer: Create consensusMatrix for codon bases by Kevin Blighe ★ 4.0k
You can achieve this by first extracting the codons from each sequence in the DNAStringSet and then counting their frequencies at each codo…
Answer: Memory error while running alignments by Kevin Blighe ★ 4.0k
Your error arises from insufficient memory allocation on your system. A distance matrix for 50,000 sequences requires substantial RAM. For …
Answer: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi by Kevin Blighe ★ 4.0k
The error that you are encountering with DESeq2 indicates that your design matrix is singular, which occurs when the number of samples equa…
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Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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
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