Showing : rnaseqdata • reset
1
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117
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Merging annotation with differential expression output
annotation RNASeqData
updated 2 days ago by 68k • written 2 days ago by • 0
0
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3
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565
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 4 weeks ago by 43k • written 5 weeks ago by • 0
0
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0
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111
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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
8 weeks ago cftattersfield • 0
0
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5
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363
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 9 weeks ago by • 0
0
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1
reply
206
views
Correlation between gene clusters
genomes RNASeqData
written 11 weeks ago by • 0
0
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2
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349
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Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
11 weeks ago gingergeiger22 • 0
2
votes
1
reply
416
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 11 weeks ago by 43k • written 3 months ago by • 0
0
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1
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261
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combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 3 months ago by • 0 • written 3 months ago by • 0
2
votes
1
reply
417
views
DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 3 months ago by 43k • written 4 months ago by • 0
0
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4
replies
772
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
5 months ago • updated 4 months ago Philippine • 0
0
votes
2
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459
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 5 months ago by • 0
3
votes
11
replies
1.0k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 5 months ago by • 0
1
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1
reply
559
views
WGCNA
DEGselection RNASeqData WGCNA
updated 5 months ago by ▴ 760 • written 5 months ago by • 0
1
vote
1
reply
353
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 5 months ago by ★ 4.8k • written 5 months ago by • 0
1
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1
reply
580
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 6 months ago by 52k • written 6 months ago by • 0
1
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2
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2.1k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 6 months ago by • 0
1
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2
replies
433
views
Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
7 months ago Gordon • 0
0
votes
3
replies
692
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 8 months ago by ★ 4.8k • written 8 months ago by • 0
0
votes
4
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746
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 8 months ago by • 0
1
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3
replies
1.4k
views
Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
9 months ago Tanvi • 0
1
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3
replies
719
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 9 months ago by 68k • written 9 months ago by ▴ 50
0
votes
1
reply
458
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 9 months ago by 68k • written 9 months ago by • 0
0
votes
1
reply
466
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 6 months ago by ▴ 20 • written 10 months ago by • 0
0
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1
reply
471
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 10 months ago by 52k • written 10 months ago by • 0
0
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1
reply
428
views
Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 11 months ago by 68k • written 12 months ago by • 0
3
votes
5
replies
1.3k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 12 months ago by 43k • written 13 months ago by ▴ 10
0
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0
replies
603
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
13 months ago Abril • 0
1
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2
replies
2.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 23 months ago by • 0
1
vote
3
replies
868
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
14 months ago island • 0
0
votes
2
replies
606
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
14 months ago Diana • 0
0
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1
reply
896
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 14 months ago by ★ 4.8k • written 14 months ago by • 0
5
votes
6
replies
1.2k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
14 months ago Shaimaa Gamal • 0
1
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1
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756
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 15 months ago by ★ 4.8k • written 15 months ago by • 0
0
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2
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893
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
15 months ago Luca • 0
0
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1
reply
1.3k
views
Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 15 months ago by 68k • written 15 months ago by • 0
1
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2
replies
900
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
15 months ago drewhaydensteele • 0
1
vote
1
reply
754
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 16 months ago by ★ 4.8k • written 16 months ago by • 0
1
vote
2
replies
1.4k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
16 months ago • updated 15 months ago Levi • 0
0
votes
3
replies
2.1k
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
16 months ago Oenone • 0
3
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4
replies
1.1k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
16 months ago pl23 • 0
0
votes
1
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626
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 16 months ago by 43k • written 16 months ago by ▴ 10
2
votes
2
replies
818
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
16 months ago Manthos • 0
0
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1
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740
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 16 months ago by ★ 13k • written 16 months ago by • 0
0
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2
replies
779
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
16 months ago Ben ▴ 10
0
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2
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2.2k
views
MA plot for DESEq2 analysis
RNASeqData DESeq2
16 months ago RHEA • 0
2
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3
replies
2.2k
views
Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
1
vote
1
reply
869
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 17 months ago by 68k • written 17 months ago by • 0
1
vote
7
replies
1.4k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 15 months ago by 52k • written 17 months ago by • 0
0
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1
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784
views
Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 17 months ago by ▴ 780 • written 18 months ago by • 0
2
votes
4
replies
1.3k
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
18 months ago Shihui • 0
50 results • Page 1 of 1
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Comment: Annotation package for Manduca sexta by GA ▴ 10
Thank you!
Comment: Improving performance of edgeR and limma while adjusting for multiple confounder by ATpoint ★ 4.8k
If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k
We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…
Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k
It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…
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Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
A: Is logFC a log2 fold change or some other base in scran::findMarkers
Comment: Error in retrieving clinical data
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