Showing : DifferentialExpression • reset
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 5 weeks ago by 51k • written 5 weeks ago by • 0
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 6 weeks ago by 67k • written 6 weeks ago by • 0
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 6 weeks ago by • 0
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 6 weeks ago by ★ 1.4k • written 7 weeks 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 9 weeks ago by ★ 4.4k • written 9 weeks ago by • 0
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 9 weeks ago by 67k • written 10 weeks ago by • 0
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
11 weeks ago nhaus ▴ 70
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 3 months ago by • 0 • written 6 months ago by ▴ 50
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 3 months ago by 67k • written 3 months ago by ▴ 70
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
3 months ago vohara4 • 0
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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 3 months ago by 67k • written 3 months ago by • 0
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339
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 4 months ago by 42k • written 4 months ago by • 0
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535
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 4 months ago by 51k • written 4 months ago by • 0
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 4 months ago by ★ 4.4k • written 4 months ago by • 0
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
4 months ago sajadahmad41454 • 0
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 4 months ago by ★ 4.4k • written 4 months ago by • 0
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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 5 months ago by 67k • written 5 months ago by • 0
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 5 months ago by 42k • written 5 months ago by ▴ 70
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6
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 5 months ago by ★ 4.4k • written 5 months ago by ▴ 70
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488
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 5 months ago by 67k • written 5 months ago by • 0
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 5 months ago by 67k • written 5 months ago by • 0
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429
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
6 months ago Chanderkant Chaudhary • 0
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 6 months ago by 51k • written 6 months ago by ▴ 50
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 6 months ago by 51k • written 6 months ago by • 0
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534
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 6 months ago by 42k • written 6 months ago by • 0
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647
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 7 months ago by • 0
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4
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579
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
7 months ago mperalc • 0
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444
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
7 months ago Abril • 0
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458
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 7 months ago by ★ 4.4k • written 7 months ago by • 0
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507
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
7 months ago Shaimaa Gamal • 0
4
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613
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 7 months ago by 51k • written 7 months ago by • 0
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594
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 7 months ago by 67k • written 7 months ago by • 0
2
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1
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 7 months ago by 42k • written 7 months ago by ▴ 20
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490
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PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 8 months ago by 42k • written 8 months ago by • 0
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
8 months ago Shaimaa Gamal • 0
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6
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939
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 7 months ago by 51k • written 8 months ago by • 0
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525
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Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 8 months ago by 51k • written 8 months ago by • 0
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820
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 9 months ago by • 0
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5
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903
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Help with model for differential expression analysis
DifferentialExpression edgeR
9 months ago • updated 8 months ago Lucy ▴ 60
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609
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DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 9 months ago by ★ 4.4k • written 9 months ago by • 0
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571
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Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 9 months ago by ★ 4.4k • written 9 months ago by • 0
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Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 8 months ago by 51k • written 9 months ago by • 0
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593
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
9 months ago Luca • 0
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2
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810
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 10 months ago by 51k • written 10 months ago by • 0
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496
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DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 10 months ago by 42k • written 10 months ago by ▴ 10
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4
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769
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rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 10 months ago by 42k • written 10 months ago by ▴ 60
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Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
11 months ago • updated 10 months ago Luca • 0
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558
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clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
11 months ago nromerov • 0
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1.0k
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Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 12 months ago by 16k • written 12 months ago by • 0
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Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
12 months ago Shihui • 0
50 results • Page 1 of 1
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Replies
Comment: How should I run ssGSEA Hallmark Enrichment Analysis? by Ginny • 0
I think the other side of this question is that the non protein coding genes would be in the "background", they would influence the ranking…
Comment: ISO a solution to rank-order introns by transcript by James W. MacDonald 67k
There's an error in the last line. Note that `sapply(lengths(z), seq_len)` will return a `list` because the lengths vary. We need a vector,…
Comment: BiomaRt - improved access to Ensembl ? by Mike Smith ★ 6.5k
Why do you want to use `useMart()` rather than `useEnsembl()`? They are essentially the same (`useEnsembl()` will eventually call `useMart(…
Comment: Installing Bioconductor packages in Docker by devarti.mahakalkar • 0
I have installed BiocManager on my base image rather than having it as base image. RUN Rscript -e "install.packages('BiocManager', re…
Comment: Meta-analysis on RNA-seq data sets by Travis • 0
Thank you for your suggestions and explanation of your approach!
Votes
Answer: ISO a solution to rank-order introns by transcript
Answer: ISO a solution to rank-order introns by transcript
Answer: Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're c
Answer: Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're c
Answer: addPatternDensity in 'qsea' takes too much time
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