Showing : RNASeqData • reset
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Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
3.1 years ago dantasezequiel1 • 0
2
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3
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1.4k
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RNA-seq analysis without replicates
DESeq2 RESEQ RNASeqData
updated 13 months ago by • 0 • written 13 months ago by • 0
0
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2
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663
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Is there any reason to think that normalization (e.g. TMM) doesn't work well with samples that that have very different raw counts?
limma RNASeqData edgeR
updated 14 months ago by ▴ 30 • written 14 months ago by • 0
1
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7
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880
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DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 5 months ago by 50k • written 7 months ago by • 0
1
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2
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1.2k
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
1
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2
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2.7k
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Understanding how to contrast two treatments in DESeq2
DESeq2 RNASeqData
updated 20 months ago by ★ 1.4k • written 20 months ago by • 0
3
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6
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1.3k
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Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 3.5 years ago by 42k • written 3.5 years ago by ▴ 50
4
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1
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2.4k
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Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2 RNASeq RNASeqData
updated 2.2 years ago by 42k • written 2.2 years ago by ▴ 30
0
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1
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802
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Differential Expression Analysis-Input is DESeq Standardized
rnaseq RNASeqData limma limmaGUI
updated 2.1 years ago by 42k • written 2.1 years ago by • 0
2
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5
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1.4k
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edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
0
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10
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2.9k
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GenomicAlignments - Speeding up readGAlignmentPairs()
Cancer RNAseqData GenomicFeatures Cancer RNAseqData GenomicFeatures
updated 9.9 years ago by ▴ 320 • written 9.9 years ago by ★ 6.8k
3
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2
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943
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Why some statistically differently expressed genes are not DEGs?
RNASeqData DEGreport edgeR
3.2 years ago Wuschel ▴ 10
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5
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2.2k
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Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData isoform DESeq2
2.1 years ago • updated 24 months ago priyanka.m • 0
6
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4
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11k
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How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 2.4 years ago by • 0 • written 3.2 years ago by ▴ 10
2
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3
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1.2k
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PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
0
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6
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810
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Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 10 months ago by 50k • written 10 months ago by • 0
0
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3
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762
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Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 15 months ago by 50k • written 15 months ago by • 0
2
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4
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1.2k
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DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData DESeq2
2.7 years ago khaveh ▴ 10
0
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2
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1.4k
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How to run vst transformation
RNASeqData vst
updated 2.0 years ago by 42k • written 2.0 years ago by • 0
1
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2
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1.6k
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Binning expression data along with capturing gene identifiers
rnaseqdata clustering
updated 9.3 years ago by ★ 2.0k • written 9.3 years ago by ▴ 150
2
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4
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2.8k
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Compare 3 RNASeq groups with no control in DESeq2
anova RNASeqData tukeyTest DESeq2
3.5 years ago ecg1g15 ▴ 20
5
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6
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602
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
4 months ago • updated 3 months ago Shaimaa Gamal • 0
1
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6
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1.4k
views
Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
3.3 years ago Seaweed • 0
0
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1
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1.1k
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RNASeq analysis - Test for effect of two variables on one (Genotype)
deseq2 multiple factor design rnaseqdata
updated 8.1 years ago by 42k • written 8.1 years ago by ▴ 80
0
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3
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733
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DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
5 months ago Oenone • 0
22
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15
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7.6k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 6 months ago by ▴ 10 • written 2.1 years ago by ▴ 50
1
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1
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661
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Strange error while running DESeq() function.
DESeq2 RNASeq RNASeqData
updated 2.2 years ago by 42k • written 2.2 years ago by ▴ 30
4
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3
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1.2k
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Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2 idep RNASeqData
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by ▴ 10
0
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2
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377
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
5 months ago Luca • 0
0
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1
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563
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How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2 RNASeqData DifferentialExpression
updated 16 months ago by ★ 4.1k • written 16 months ago by • 0
0
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2
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797
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Extend comparisons between two groups to more groups in DESEQ2
edgeR DEGs DESEQ2 RNASeqData
2.3 years ago Raito92 ▴ 60
0
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6
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1.2k
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while doing co-expression network analysis, I am getting an error
RNASeqData
3.1 years ago Rishav ▴ 20
7
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5
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3.5k
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Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
3.5 years ago ecg1g15 ▴ 20
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3
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7.5k
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Package ‘#####’ was installed before R 4.0.0: please re-install it
Bioconductor RNASeqData DESeq2 Rsubread
updated 3.5 years ago by 65k • written 3.5 years ago by • 0
2
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8
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2.4k
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While trying to remove non differentially expressed genes through limma, I am getting a warning
RNASeqData
updated 3.1 years ago by 50k • written 3.1 years ago by ▴ 20
0
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1
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586
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Controlling for covariates and identifying DEGs using DESeq2
RNASeqData DESeq2
updated 10 months ago by 42k • written 10 months ago by ▴ 20
1
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2
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541
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I changed the reference in DGE contrasts by DESeq2, but the results changed just a bit and not in the sign of Log2FC (positive to negative and invers…
RNASeqData DESeq2
updated 10 months ago by 42k • written 10 months ago by • 0
1
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4
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1.1k
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lncRNA Differential Expression Analysis
DESeq2 limma RNASeqData
2.1 years ago sushimoto • 0
0
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4
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688
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filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 8 months ago by 65k • written 8 months ago by ▴ 10
1
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1
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402
views
Deseq contrast question
RNASeqData DESeq2
updated 11 months ago by 42k • written 11 months ago by ▴ 10
2
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9
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2.3k
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Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
23 months ago Peipei • 0
1
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4
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1.3k
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Inverted Log2FC values after DEseq2 analysis
DESeq2 Log2FC RNASeqData
16 months ago Iwan • 0
3
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3
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1.4k
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How to formulate 2 factor nested design in DESeq2
nested_design RNASeqData DESeq2
24 months ago • updated 23 months ago JK Kim ▴ 20
0
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1
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653
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HSMMSingleCell metadata
ExperimentHubData ExpressionData CellDataSet RNASeqData
2.2 years ago karl.stamm ▴ 10
0
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1
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178
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 17 days ago by 50k • written 17 days ago by • 0
1
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1
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1.2k
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Help understanding edgeR code for doing exactTest
exacttest RNASeqData edgeR diffGeneAnalysis
updated 2.6 years ago by 50k • written 2.6 years ago by • 0
1
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1
reply
354
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
1
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2
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692
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Installation of R-packages for RNA-seq analysis
RNASeqData
15 months ago Begin-R • 0
0
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2
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643
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RNA-Seq and disease outcome analysis
rnaseqAnalysis RNASeqData
15 months ago JonasEnder • 0
1
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1
reply
615
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DESEQ2 differential expression for subsets of data?
RNASeqData DESeq2
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
50 results • Page 1 of 1
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Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by robersy • 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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