Showing : rnaseqdata • reset
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DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 29 days ago by ★ 4.8k • written 4 weeks ago by • 0
1
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1
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188
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Merging annotation with differential expression output
annotation RNASeqData
updated 4 weeks ago by 68k • written 4 weeks ago by • 0
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3
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617
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
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0
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145
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My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing RNASeqData DEXSeq
12 weeks ago cftattersfield • 0
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5
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429
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 3 months ago by • 0
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1
reply
265
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Correlation between gene clusters
genomes RNASeqData
written 3 months ago by • 0
0
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2
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411
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Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
3 months ago gingergeiger22 • 0
2
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1
reply
456
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 3 months ago by 43k • written 4 months ago by • 0
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1
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309
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combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 4 months ago by • 0 • written 4 months ago by • 0
2
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1
reply
478
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 4 months ago by 43k • written 5 months ago by • 0
0
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4
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814
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
6 months ago Philippine • 0
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2
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508
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 6 months ago by • 0
3
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11
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1.1k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 6 months ago by • 0
1
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1
reply
626
views
WGCNA
DEGselection RNASeqData WGCNA
updated 6 months ago by ▴ 760 • written 6 months ago by • 0
1
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1
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389
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 6 months ago by ★ 4.8k • written 6 months ago by • 0
1
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1
reply
648
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 7 months ago by 52k • written 7 months ago by • 0
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2
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2.4k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 7 months ago by • 0
1
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2
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476
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Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
8 months ago Gordon • 0
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3
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757
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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 months ago by ★ 4.8k • written 9 months ago by • 0
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4
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808
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 9 months ago by • 0
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3
replies
1.5k
views
Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
10 months ago Tanvi • 0
1
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3
replies
776
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 10 months ago by 68k • written 10 months ago by ▴ 50
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1
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481
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 10 months ago by 68k • written 10 months ago by • 0
0
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1
reply
486
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 7 months ago by ▴ 20 • written 11 months ago by • 0
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1
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494
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 12 months ago by 52k • written 12 months ago by • 0
0
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1
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467
views
Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 13 months ago by 68k • written 13 months ago by • 0
3
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5
replies
1.4k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 14 months ago by 43k • written 14 months ago by ▴ 10
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0
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628
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
14 months ago Abril • 0
1
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2
replies
2.2k
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 24 months ago by • 0
1
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3
replies
926
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
15 months ago island • 0
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2
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630
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ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
15 months ago Diana • 0
0
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1
reply
936
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 15 months ago by ★ 4.8k • written 15 months ago by • 0
5
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6
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1.2k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
15 months ago Shaimaa Gamal • 0
1
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1
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789
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Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 16 months ago by ★ 4.8k • written 16 months ago by • 0
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2
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944
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
16 months ago Luca • 0
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1
reply
1.4k
views
Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 16 months ago by 68k • written 16 months ago by • 0
1
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2
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958
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RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
17 months ago drewhaydensteele • 0
1
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1
reply
783
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 17 months ago by ★ 4.8k • written 17 months ago by • 0
1
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2
replies
1.5k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
17 months ago • updated 16 months ago Levi • 0
0
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3
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2.2k
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
17 months ago Oenone • 0
3
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4
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1.1k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
17 months ago pl23 • 0
0
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1
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640
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DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 17 months ago by 43k • written 17 months ago by ▴ 10
2
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2
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857
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DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
17 months ago Manthos • 0
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1
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761
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DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 17 months ago by ★ 13k • written 17 months ago by • 0
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2
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800
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Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
17 months ago Ben ▴ 10
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2
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2.3k
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MA plot for DESEq2 analysis
RNASeqData DESeq2
17 months ago RHEA • 0
2
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3
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2.3k
views
Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 18 months ago by ★ 1.4k • written 18 months ago by • 0
1
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1
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896
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 18 months ago by 68k • written 18 months ago by • 0
1
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7
replies
1.4k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 17 months ago by 52k • written 18 months ago by • 0
0
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1
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811
views
Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 19 months ago by ▴ 780 • written 19 months ago by • 0
50 results • Page 1 of 1
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Comment: Bioconductor 3.20 Release Schedule by randyprice13102000 • 0
This offers much info https://bioconductor.org/checkResults/release/bioc-LATEST/
Comment: Filtering after DESeq by ATpoint ★ 4.8k
The problem is that your prefilter is not group-aware so the behaviour of seeing these sorts of outliers is expected. This is why I always …
Comment: GSEA preranked analysis downstream of DEseq2 by ATpoint ★ 4.8k
All due respect, this is what people do since pvalues exist, so this paper is not a reference, not is this a special score that merits a na…
Comment: Check removeBatchEffect effectiveness by ATpoint ★ 4.8k
> insert size, mean GC, etc... This is not a classical "batch" in the common sense, at least I've never seen this to be corrected for expl…
Answer: Check removeBatchEffect effectiveness by Gordon Smyth 52k
Your call to removeBatchEffect() is not correct because that function does not have an argument called `batch3`, meaning that the batch fac…
Votes
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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