Showing : DESEQ2 • reset
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Using multiple covariates in DIffBind
DiffBind Deseq2
updated 5.0 years ago by ★ 5.2k • written 5.7 years ago by ▴ 10
4
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3
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1.5k
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Diffbind for regressing multiple confounding variables (blocking factors)
diffbind block regression deseq2 chipseq
updated 5.0 years ago by ★ 5.2k • written 6.1 years ago by ▴ 10
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3
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1.8k
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DESeq2 data input
DESeq2
updated 4.0 years ago by 43k • written 5.0 years ago by • 0
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1
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1.7k
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How to prepare a file to DESeq2 analysis?
DESeq2
updated 5.0 years ago by ★ 1.4k • written 5.0 years ago by • 0
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4
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1.4k
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DESeq2: Model matrix problem with 30 samples
DESeq2 RNAseq
5.1 years ago • updated 5.0 years ago dagurim • 0
2
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2
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895
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Different results if "treated/untreated" is switched to "untreated/treated" with apeglm
DESeq2
5.0 years ago serdarT • 0
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10
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2.8k
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Do I have clustering by library size?
PCA DESeq2 Normalization librarysize
updated 5.0 years ago by 43k • written 5.1 years ago by ▴ 10
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4
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1.6k
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Walt Test 2 factors
WaldTest_2factors DESeq2
5.1 years ago • updated 5.0 years ago julie • 0
3
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6
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4.2k
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DESeq2: When to split multiple group samples for 'more' accurate sizefactors, dispersions etc.
Dispersion RNA-seq DESeq2 Multiple-group
updated 4.8 years ago by 43k • written 5.1 years ago by ▴ 10
34
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29
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17k
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[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 14 months ago by 43k • written 10.7 years ago by ▴ 130
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1
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868
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DESeq2 Handling Multiple Biological templates
DESeq2
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
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1
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655
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Using DESEQ/EdgeR for estimating differential expression relative to a control.
edgeR DifferentialExpression
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
2
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1
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1.0k
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How to extract top DEG and their sample values
DESeq2 RNASeq
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by ▴ 30
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1
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747
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correlation analysis
Hmisc
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 40
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12
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5.7k
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Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2 deseq
updated 5.1 years ago by 43k • written 10.5 years ago by • 0
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4
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1.1k
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Using DESeq with 2 assays having 2 conditions
DESeq2
5.1 years ago ludovic.malet • 0
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4
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1.9k
views
Raw reads count matrix from exceRpt pipeline are not integers which is needed for Deseq2
DESeq2 exceRpt exRNA
updated 5.1 years ago by ★ 1.1k • written 5.1 years ago by ▴ 10
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3
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1.6k
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Weird set of samples in plant gene atlas study that appear over-corrected after DESeq2 normalization
RNA-Seq DESeq2
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
0
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11
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2.8k
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DESeq2 --- differences in log2FC between results from DESeq() command and nbinomLRT() command
deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
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1.2k
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p-value/p-adj value as 0
deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
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4
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1.2k
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DESeq2 different datasets
deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
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3
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1.5k
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DESeq2 multiple groups comparison issues, incorrect log2FC results in a small proportion of genes
deseq2
updated 5.0 years ago by 43k • written 5.1 years ago by • 0
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1
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1.1k
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DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2 design formula
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 50
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5
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2.8k
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DeSeq2 with three batches - Remove batch Effect
deseq2 batch removebatch effect
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 50
2
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2
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1.2k
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Fold Change and Technical Details of DESeq2
deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 10
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3
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1.9k
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Deseq2 Biological replicates and nested conditions
deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
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5
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1.3k
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DESeq2 Normalization causing overcorrection in libaries sizes for a few samples
deseq2 normalization
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
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0
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1.4k
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Job: Two bioinformatics positions at Boston Children's Hospital
NGS Job
updated 5.0 years ago by 43k • written 5.1 years ago by • 0
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1
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2.8k
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importing RSEM data into DESeq2
deseq2 tximport
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 10
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2
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2.3k
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prefiletring before PCA and DESeq2 DE analysis
deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 50
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4
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1.9k
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DESeq2 interaction design with factor containing multiple levels
deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
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5
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1.5k
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Is it capable to analysis the unbalanced time course experiment by DESeq2?
time course deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
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9
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4.1k
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How to create manhattan plot with DESeq2
deseq2 mahattan plot RNA Seq
updated 5.1 years ago by ▴ 150 • written 6.1 years ago by • 0
0
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2
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952
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Multi-design batches analysis DESeq2
deseq2
5.1 years ago Sedlin • 0
3
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5
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2.4k
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overshrinkage of LFC with apeglm
deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 10
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1
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704
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DESeq2 and shrinkage
deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
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5
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2.0k
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DESeq2 library composition adjustment in size factors
deseq2 normalization
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
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4
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648
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n of 1 exploratory analysis
deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
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1
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2.2k
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Are DESeq2 significant results with 2 replicates per group, less than significant results with more replicates?
deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 30
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7
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DESeq2::rlogTransformation missing rownames vs vst.
deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
0
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2
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1.1k
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Design for multi-factor problem with DESeq2
deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
7
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9
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21k
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Contrasts in DESeq2
deseq2 contrast
updated 3.3 years ago by • 0 • written 5.1 years ago by ▴ 60
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2
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1.1k
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Convergence of betas, iterations arguments with nbinomialWaldTest
deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 30
4
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5
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2.1k
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one group against two other groups comparison using LRT test (pseudobulk approach)
deseq2
5.1 years ago • updated 4.8 years ago amel.zulji ▴ 20
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6
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1.2k
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Single model matrix_design formula_RNASeq_DESeq2
deseq2
5.1 years ago bhanu.chandra1 • 0
1
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5
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1.6k
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CyTOF Differential Abundance Analysis using DESeq2
deseq2 mass cytometry CyTOF
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 280
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1
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342
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How to compare the paired value
deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
2
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3
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725
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DEseq2: DESeq function not correcting for batch variable
deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
1
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2
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1.7k
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Re-calculation of Padj (P adjusted value)
statistics Benjamini–Hochberg procedure deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 60
0
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4
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1.1k
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Paired analysis DESeq2 problems
DESeq2
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 10
4,839 results • Page 35 of 97
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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: 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…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
The issue that you describe with the tumor mutational burden (TMB) plots appearing linear and lacking consistent TMB values across samples …
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Kevin Blighe ★ 4.0k
There are alternative explanations for why these samples are so similar. The similarity could result from low biological variability in gen…
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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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