Showing : RNASeqData • reset
0
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106
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Correlation between gene clusters
genomes RNASeqData
written 14 days ago by • 0
0
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2
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210
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Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
15 days ago • updated 14 days ago gingergeiger22 • 0
2
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1
reply
337
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 16 days ago by 43k • written 24 days ago by • 0
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1
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173
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combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 25 days ago by • 0 • written 27 days ago by • 0
1
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1
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278
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 6 weeks ago by 43k • written 8 weeks ago by • 0
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4
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657
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
12 weeks ago Philippine • 0
0
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2
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375
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 3 months ago by • 0
3
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11
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816
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 3 months ago by • 0
1
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1
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408
views
WGCNA
DEGselection RNASeqData WGCNA
updated 3 months ago by ▴ 760 • written 3 months ago by • 0
1
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1
reply
282
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 3 months ago by ★ 4.6k • written 3 months ago by • 0
1
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1
reply
492
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 4 months ago by 52k • written 4 months ago by • 0
1
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2
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1.3k
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How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 4 months ago by • 0
1
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2
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360
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Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
4 months ago Gordon • 0
0
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3
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614
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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 6 months ago by ★ 4.6k • written 6 months ago by • 0
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4
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636
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 6 months ago by • 0
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3
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1.1k
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
7 months ago Tanvi • 0
1
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3
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617
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 7 months ago by 67k • written 7 months ago by ▴ 50
0
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1
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391
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 7 months ago by 67k • written 7 months ago by • 0
0
votes
1
reply
396
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 4 months ago by ▴ 20 • written 8 months ago by • 0
0
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1
reply
416
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 8 months ago by 52k • written 8 months ago by • 0
0
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1
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354
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Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 9 months ago by 67k • written 9 months ago by • 0
3
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5
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1.2k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 months ago by 43k • written 11 months ago by ▴ 10
0
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0
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540
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
11 months ago Abril • 0
1
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2
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1.9k
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 20 months ago by • 0
1
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3
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737
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
11 months ago island • 0
0
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2
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541
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
12 months ago • updated 11 months ago Diana • 0
0
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1
reply
787
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 12 months ago by ★ 4.6k • written 12 months ago by • 0
5
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6
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1.0k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
12 months ago Shaimaa Gamal • 0
1
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1
reply
681
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 13 months ago by ★ 4.6k • written 13 months ago by • 0
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2
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788
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
13 months ago Luca • 0
0
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1
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1.1k
views
Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 13 months ago by 67k • written 13 months ago by • 0
1
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2
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809
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RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
13 months ago drewhaydensteele • 0
1
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1
reply
667
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 13 months ago by ★ 4.6k • written 13 months ago by • 0
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2
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1.3k
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Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
13 months ago Levi • 0
0
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3
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1.7k
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DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
13 months ago Oenone • 0
3
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4
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1.0k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
14 months ago pl23 • 0
0
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1
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564
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DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 14 months ago by 43k • written 14 months ago by ▴ 10
2
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2
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731
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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
14 months ago Manthos • 0
0
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1
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670
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 14 months ago by ★ 13k • written 14 months ago by • 0
0
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2
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717
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Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
14 months ago Ben ▴ 10
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2
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1.8k
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MA plot for DESEq2 analysis
RNASeqData DESeq2
14 months ago RHEA • 0
2
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3
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1.8k
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Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 15 months ago by ★ 1.4k • written 15 months ago by • 0
1
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1
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760
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 15 months ago by 67k • written 15 months ago by • 0
1
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7
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1.3k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 13 months ago by 52k • written 15 months ago by • 0
0
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1
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704
views
Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 15 months ago by ▴ 780 • written 15 months ago by • 0
2
votes
4
replies
1.2k
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
16 months ago • updated 15 months ago Shihui • 0
0
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4
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1.1k
views
filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 16 months ago by 67k • written 16 months ago by ▴ 10
3
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3
replies
2.6k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
16 months ago Ethan Nguyen • 0
1
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1
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1.2k
views
Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 16 months ago by 67k • written 16 months ago by • 0
0
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2
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853
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RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
16 months ago Beyza • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Comment: EdgeR Biological CVs by ATpoint ★ 4.6k
"Joseph" is a spam bot...
Answer: How to sort negative log2FC or FC in RNAseq for GSEA? by ATpoint ★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
Comment: EdgeR Biological CVs by James • 0
Thank you Gordon and Joseph. I presume question (1) would be answered by using a prior G0 of 0? For question (2), I was expecting a biolog…
Comment: EdgeR Biological CVs by Joseph ▴ 10
I believe the published study provides answers to your questions. Yunshun Chen and Pedro Baldoni's recent papers on edgeR may also be of in…
Votes
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Comment: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
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