Showing : DESEQ2 • reset
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DESeq analysis with Biological replicate.
DESeq2 ExpressionData GeneExpression
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
4
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6
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9.1k
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DEseq2 comparison order
DESeq2
4.8 years ago blur ▴ 10
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0
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1.2k
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Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
4.8 years ago wrzl • 0
0
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1
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850
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Defining Factors in DESeq2
DESeq2
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
1
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2
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1.8k
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differential loop using DESeq2
hichip DESeq2 fithichip differentialloop
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
0
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8
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1.6k
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htseq counts raw data preparation for DESeq2 input file
DESeq2
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
0
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9
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4.2k
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Failed to find a rowRanges() method
DESeq2
updated 3.4 years ago by ▴ 10 • written 4.8 years ago by • 0
4
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14
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2.6k
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DESeq2: Significant padj and LFC in a 0 vs. 20 counts comparison?
DESeq2
updated 4.8 years ago by • 0 • written 4.8 years ago by ▴ 30
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1
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3.7k
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DESeq2 time course analysis
DESeq2 Timecourse
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
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5
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1.1k
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Unexpected results
resultsNames DESeq2
written 4.8 years ago by ▴ 10
4
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4
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2.7k
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log2 Fold Change in DESeq2 is not identical to FC calculated from normalized count when betaPrior is turned off
DESeq2
4.8 years ago Yanling ▴ 10
0
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2
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1.1k
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Design Matrix for DESeq2 or EdgeR
edgeR DESeq2 RNASeq
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
16
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19
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22k
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DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
updated 3.8 years ago by ▴ 60 • written 11.1 years ago by ▴ 130
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3
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2.8k
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Normalization for two bulk RNA datasets with different library sizes
Normalization BulkRNA-seq DESeq2
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
0
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6
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2.1k
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Unexpected gene polymorphism using Salmon-tximeta-DESeq2
tximeta DESeq2
4.9 years ago • updated 4.8 years ago Ray ▴ 20
0
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1
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659
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Using Deseq2 for RNA-seq analysis of 4 different groups of cells
DESeq2 RNASeq
updated 4.9 years ago by ★ 5.0k • written 4.9 years ago by • 0
0
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3
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1.8k
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Does DiffBind correctly designate peaks with very small fold-change to be statistically significant?
DESeq2 DiffBind
updated 4.5 years ago by ★ 5.2k • written 4.9 years ago by ▴ 10
3
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11
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4.5k
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DESeqDataSetFromMatrix gives a 'dimnames are not identical error' in R 4.0 that worked fine in R 3.6.1.
DESeq2 SummarizedExperiment
updated 3.3 years ago by • 0 • written 4.9 years ago by ▴ 20
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3
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1.5k
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Using altHypothesis on apleglm-shrunken log2FoldChanges
apeglm DESeq2
4.9 years ago zefrieira • 0
1
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1
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1.5k
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DEseq2 complex design - 2 factors with more than 2 levels
DESeq2
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 20
1
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11
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3.5k
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Using the correct counts with lm function linear model
lm DESeq2
updated 4.9 years ago by ▴ 10 • written 4.9 years ago by ▴ 50
3
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5
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1.5k
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Validation of DESeq2 v1.30 results
DESeq2
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
0
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3
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915
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Strange patterns in Log2fold change output
DESeq2
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
2
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2
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1.6k
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Design formula for pairwise comparison of experimental setup with multiple factors
DEGs DESeq2
4.9 years ago 2021yearsold • 0
0
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1
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1.5k
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DESeq2 - shrunken LFC calculation
apeglm DESeq2
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 50
1
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7
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2.7k
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Weird results after lfc command (shrinkage)
lfcshrinkage DESeq2
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
0
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1
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658
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DESeq2 paired design with missing samples
missingdata DESeq2 paired-sample
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
2
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8
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4.2k
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How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 23 months ago by • 0 • written 4.9 years ago by ▴ 20
4
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4
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1.2k
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Something strange in the ranking of genes by DESeq2
DESeq2
4.9 years ago Dejian Zhao ▴ 10
0
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3
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1.8k
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Using transformed matrix in DESeq2
DESeq2 VST
updated 4.9 years ago by ★ 5.0k • written 4.9 years ago by • 0
2
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3
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11k
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DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by ▴ 30
6
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8
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3.6k
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Interaction with DESeq2 via DiffBind
diffbind deseq2 interactions
updated 4.9 years ago by • 0 • written 8.1 years ago by ▴ 60
0
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1
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1.1k
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Matrix not full rank (time-series experiment with one group and covariates )
DESeq2 DES
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 10
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1
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1.1k
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DESeq2 interactions genotype condition code needed
DESeq2 anova condition genotypeeval
updated 4.9 years ago by ★ 5.0k • written 4.9 years ago by ▴ 20
0
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7
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2.8k
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Error while running DE in DESeq2
DESeq2
updated 4.2 years ago by • 0 • written 4.9 years ago by • 0
0
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1
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653
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Group-specific treatment effect
DESeq2 differentialexpressionanalysis
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
5
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4
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4.7k
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Dispersion Estimates and MA plots
DESeq2
4.9 years ago hazwanfikri0505 ▴ 20
0
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2
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1.3k
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Differential expression on RNAseq without replicates
DESeq2 NOISeq edgeR
updated 4.9 years ago by ★ 5.0k • written 4.9 years ago by • 0
3
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3
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1.2k
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Rename rownames(res) manually
DESeq2
4.9 years ago E. Marina ▴ 10
3
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2
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2.0k
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Self-contained gene set testing with DESeq2 results
roast DESeq2 GeneSetEnrichment
updated 4.9 years ago by 53k • written 4.9 years ago by • 0
0
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1
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846
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DESeq2 paired analysis matrix
DESeq2
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 10
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2
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3.3k
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DESeq2 counts as input for WGCNA
WGCNA DESeq2
4.9 years ago Peny • 0
2
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9
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2.3k
views
library(HTSFilter) says that "HTSFilter" does not exist
DESeq2 HTSFilter
updated 4.9 years ago by ▴ 80 • written 4.9 years ago by • 0
1
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3
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1.6k
views
Error in Differential Expression Analysis with Data Set from Matrix
DESeq2 DifferentialExpression Bioconductor
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
3
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4
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3.3k
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Cut&Run normalization for Diffbind and DESeq2
GenomicLocalization DESeq2 Cut&Run Diffbind Normalization
4.9 years ago Monica ▴ 20
0
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1
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1.1k
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Function createExpressionSet: Creating an ExpressionSet - Which package needed?
ExpressionData
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 50
0
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2
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896
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DESEQ2 Differential Expression controlling for two factors
DESeq2
updated 4.9 years ago by ★ 5.0k • written 4.9 years ago by ▴ 50
5
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6
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5.0k
views
How to add a column to metadata in SummarizedExperiment for DESeq2 type objects?
DESeq2 SummarizedExperiment
5.0 years ago • updated 4.9 years ago mschmidt ▴ 10
0
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6
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1.4k
views
how to toggle b/w forking and no forking in DESeq2
DESeq2
updated 4.9 years ago by 25k • written 5.0 years ago by • 0
2
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3
replies
3.2k
views
DESEQ2 coldata creation from featureCounts and row.names length error
DESeq2
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
4,839 results • Page 33 of 97
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Comment: Bioconductor 3.22 Release Schedule by loganlstevens • 0
This release reminds me of the strategies in [solitaired](https://solitaired.io) to overcome live solitaires.
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…
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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