Showing : differentialexpression • reset
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 5 weeks ago by 43k • written 5 weeks ago by • 0
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1
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162
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 6 weeks ago by 43k • written 7 weeks ago by • 0
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238
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 8 weeks ago by 43k • written 8 weeks ago by • 0
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5
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377
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 9 weeks ago by • 0
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
3 months ago Tadeoye ▴ 20
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1.1k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 3 months ago by 68k • written 4 months ago by • 0
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3
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651
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 4 months ago by 52k • written 4 months ago by • 0
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570
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
4 months ago abadgerw • 0
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5
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837
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
4 months ago • updated 3 months ago abadgerw • 0
0
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1
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300
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 5 months ago by 43k • written 5 months ago by • 0
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6
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1.1k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 5 months ago by 43k • written 5 months ago by • 0
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3
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673
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 7 months ago by 52k • written 7 months ago by • 0
3
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3
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1.1k
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 7 months ago by 68k • written 7 months ago by • 0
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3
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707
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 7 months ago by • 0
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5
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1.6k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 7 months ago by ★ 1.4k • written 7 months ago by • 0
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Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 8 months ago by ★ 4.8k • written 8 months ago by • 0
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 8 months ago by 68k • written 8 months ago by • 0
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574
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
8 months ago nhaus ▴ 70
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5
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2.4k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 9 months ago by • 0 • written 13 months ago by ▴ 60
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1
reply
583
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 9 months ago by 68k • written 9 months ago by ▴ 70
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4
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778
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
9 months ago vohara4 • 0
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1
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458
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How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 9 months ago by 68k • written 9 months ago by • 0
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3
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535
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 10 months ago by 43k • written 10 months ago by • 0
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3
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796
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 10 months ago by 52k • written 10 months ago by • 0
0
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1
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463
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 10 months ago by ★ 4.8k • written 10 months ago by • 0
2
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7
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1.4k
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
10 months ago sajadahmad41454 • 0
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3
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1.1k
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 11 months ago by ★ 4.8k • written 11 months ago by • 0
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3
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662
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Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 11 months ago by 68k • written 11 months ago by • 0
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2
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625
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 11 months ago by 43k • written 11 months ago by ▴ 70
5
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6
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1.1k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 11 months ago by ★ 4.8k • written 11 months ago by ▴ 70
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3
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656
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 11 months ago by 68k • written 11 months ago by • 0
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641
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 11 months ago by 68k • written 11 months ago by • 0
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2
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612
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
12 months ago Chanderkant Chaudhary • 0
8
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5
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2.3k
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 5 months ago by 52k • written 12 months ago by ▴ 60
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660
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 12 months ago by 52k • written 12 months ago by • 0
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2
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875
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 12 months ago by 43k • written 12 months ago by • 0
1
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3
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833
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 14 months ago by • 0
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4
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791
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
13 months ago mperalc • 0
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0
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606
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
13 months ago Abril • 0
2
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1
reply
600
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 13 months ago by ★ 4.8k • written 13 months ago by • 0
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700
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
13 months ago Shaimaa Gamal • 0
4
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3
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880
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 13 months ago by 52k • written 13 months ago by • 0
2
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3
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813
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 13 months ago by 68k • written 13 months ago by • 0
2
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1
reply
541
views
Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 14 months ago by 43k • written 14 months ago by ▴ 20
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2
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632
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PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 14 months ago by 43k • written 14 months ago by • 0
5
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6
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1.2k
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
14 months ago Shaimaa Gamal • 0
4
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6
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1.3k
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 13 months ago by 52k • written 14 months ago by • 0
3
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1
reply
673
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 14 months ago by 52k • written 14 months ago by • 0
1
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3
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1.0k
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 15 months ago by • 0
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5
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1.1k
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Help with model for differential expression analysis
DifferentialExpression edgeR
15 months ago • updated 14 months ago Lucy ▴ 60
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Comment: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran by Arctic • 0
Many thanks for the link to the C++ code. I will see if I can find someone with C++ experience to help me with the code breakdown from her…
Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran by Aaron Lun ★ 28k
It's calling C++ code, see the relevant function definitions on [GitHub](https://github.com/knncolle/BiocNeighbors/blob/master/src/generics…
Answer: DESeq2 by ATpoint ★ 4.8k
Time courses are often inevitable batches but you should have done the library prep at the same day, just extract RNA per day. If not then …
Comment: Package developing and interoperation with Bioconductor by slizchap • 0
Thank you so much for your answer. This was very useful, I will optimize my functions so they can handle SE objects.
Comment: Package developing and interoperation with Bioconductor by slizchap • 0
Thank you so much for your answer, very useful!
Votes
Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran
Is it possible to speed up VariantAnnotation's rowRanges function when converting to a dataframe?
Answer: Is it possible to speed up VariantAnnotation's rowRanges function when convertin
Comment: ComBat with repeated measures
Answer: Package developing and interoperation with Bioconductor
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