Showing : rnaseqdata • reset
0
votes
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54
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Correlation between gene clusters
genomes RNASeqData
written 1 day ago by • 0
0
votes
2
replies
118
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Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
2 days ago • updated 11 hours ago gingergeiger22 • 0
2
votes
1
reply
240
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 3 days ago by 43k • written 11 days ago by • 0
0
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1
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144
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combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 11 days ago by • 0 • written 14 days ago by • 0
1
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1
reply
257
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 5 weeks ago by 43k • written 6 weeks ago by • 0
0
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4
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645
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
10 weeks ago Philippine • 0
0
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2
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366
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 10 weeks ago by • 0
3
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11
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793
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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
reply
374
views
WGCNA
DEGselection RNASeqData WGCNA
updated 3 months ago by ▴ 760 • written 3 months ago by • 0
1
vote
1
reply
270
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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
478
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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1.2k
views
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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347
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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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600
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 5 months ago by ★ 4.6k • written 5 months ago by • 0
0
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4
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619
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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
1
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3
replies
1.0k
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
6 months ago Tanvi • 0
1
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3
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598
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 6 months ago by 67k • written 6 months ago by ▴ 50
0
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1
reply
380
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
383
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 4 months ago by ▴ 20 • written 7 months ago by • 0
0
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1
reply
405
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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341
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Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 9 months ago by 67k • written 9 months ago by • 0
3
votes
5
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1.2k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 months ago by 43k • written 10 months ago by ▴ 10
0
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0
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522
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
10 months ago Abril • 0
1
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2
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1.8k
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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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721
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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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531
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
11 months ago Diana • 0
0
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1
reply
769
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 11 months ago by ★ 4.6k • written 11 months ago by • 0
5
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6
replies
1.0k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
11 months ago Shaimaa Gamal • 0
1
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1
reply
666
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 12 months ago by ★ 4.6k • written 12 months ago by • 0
0
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2
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769
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
13 months ago • updated 12 months ago Luca • 0
0
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1
reply
1.0k
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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795
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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
660
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 13 months ago by ★ 4.6k • written 13 months ago by • 0
1
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2
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1.2k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
13 months ago • updated 12 months ago Levi • 0
0
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3
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1.6k
views
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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989
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
13 months ago pl23 • 0
0
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1
reply
556
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 13 months ago by 43k • written 13 months ago by ▴ 10
2
votes
2
replies
723
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
13 months ago Manthos • 0
0
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1
reply
659
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 13 months ago by ★ 13k • written 14 months ago by • 0
0
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2
replies
705
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
14 months ago Ben ▴ 10
0
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2
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1.7k
views
MA plot for DESEq2 analysis
RNASeqData DESeq2
14 months ago RHEA • 0
2
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3
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1.8k
views
Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 14 months ago by ★ 1.4k • written 14 months ago by • 0
1
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1
reply
745
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 14 months ago by 67k • written 14 months ago by • 0
1
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7
replies
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
votes
1
reply
695
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
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 15 months ago by 67k • written 15 months ago by ▴ 10
3
votes
3
replies
2.5k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
15 months ago Ethan Nguyen • 0
1
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1
reply
1.2k
views
Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 15 months ago by 67k • written 15 months ago by • 0
0
votes
2
replies
832
views
RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
16 months ago Beyza • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: How do I fix an odd voom plot in a combined dataset? by 1sunmic2 • 0
So I changed it to ~0 + group (with the same plot), but I still don't know if it's good or what to fix if not.
Answer: Newbie Question - adding metadata to an analysis by James W. MacDonald 67k
See [Section 4][1]. But do note that you do not need for the `phenoData` slot to contain the data. You can simply have a 'targets' data.fra…
Comment: Want numbers in DESeq to be seen as numerical, not categorical by swbarnes2 ★ 1.4k
How did you import the data? Did you accidently leave in `stringAsFactors=True`? But I'm not entirely sure that you don't want that to be…
Comment: MissMethyl failed to use gometh function for EPICv2 by James W. MacDonald 67k
By version 1.38.0, I mean version 1.38.0 of `MissMethyl`.
Answer: MissMethyl failed to use gometh function for EPICv2 by James W. MacDonald 67k
You need to [upgrade to the release version of Bioconductor][1]. You have version 1.38.0 installed which indicates that you are using the p…
Votes
Comment: How do I fix an odd voom plot in a combined dataset?
Comment: How do I fix an odd voom plot in a combined dataset?
Comment: Theoretical WGCNA Question
Answer: Is it possible to work with DESeq2 where data is not properly matched for sex a
Answer: Is it possible to work with DESeq2 where data is not properly matched for sex a
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