Showing : RNASeqData • reset
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DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 7 weeks ago by ★ 4.8k • written 7 weeks ago by • 0
1
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1
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267
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Merging annotation with differential expression output
annotation RNASeqData
updated 7 weeks ago by 68k • written 7 weeks ago by • 0
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3
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656
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 12 weeks ago by 43k • written 12 weeks ago by • 0
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0
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162
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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
3 months ago cftattersfield • 0
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5
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453
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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
300
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Correlation between gene clusters
genomes RNASeqData
written 4 months ago by • 0
0
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2
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436
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Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
4 months ago gingergeiger22 • 0
2
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1
reply
480
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 4 months ago by 43k • written 4 months ago by • 0
0
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1
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341
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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
votes
1
reply
511
views
DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 5 months ago by 43k • written 5 months ago by • 0
0
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4
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828
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
6 months ago Philippine • 0
0
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2
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539
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 6 months ago by • 0
3
votes
11
replies
1.1k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 7 months ago by • 0
1
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1
reply
657
views
WGCNA
DEGselection RNASeqData WGCNA
updated 7 months ago by ▴ 760 • written 7 months ago by • 0
1
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1
reply
402
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 7 months ago by ★ 4.8k • written 7 months ago by • 0
1
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1
reply
677
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 8 months ago by 52k • written 8 months ago by • 0
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2
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2.6k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 8 months ago by • 0
1
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2
replies
496
views
Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
8 months ago Gordon • 0
0
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3
replies
767
views
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
0
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4
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829
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DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 10 months ago by • 0
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3
replies
1.6k
views
Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
11 months ago Tanvi • 0
1
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3
replies
790
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 11 months ago by 68k • written 11 months ago by ▴ 50
0
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1
reply
494
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 11 months ago by 68k • written 11 months ago by • 0
0
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1
reply
497
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 8 months ago by ▴ 20 • written 12 months ago by • 0
0
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1
reply
508
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 12 months ago by 52k • written 12 months ago by • 0
0
votes
1
reply
480
views
Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 13 months ago by 68k • written 13 months ago by • 0
3
votes
5
replies
1.4k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 14 months ago by 43k • written 15 months ago by ▴ 10
0
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0
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639
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
15 months ago Abril • 0
1
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2
replies
2.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.0 years ago by • 0
1
vote
3
replies
951
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
15 months ago island • 0
0
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2
replies
638
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
15 months ago Diana • 0
0
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1
reply
961
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 16 months ago by ★ 4.8k • written 16 months ago by • 0
5
votes
6
replies
1.2k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
16 months ago Shaimaa Gamal • 0
1
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1
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801
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Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 17 months ago by ★ 4.8k • written 17 months ago by • 0
0
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2
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971
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
17 months ago Luca • 0
0
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1
reply
1.4k
views
Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 17 months ago by 68k • written 17 months ago by • 0
1
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2
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990
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
17 months ago drewhaydensteele • 0
1
vote
1
reply
800
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
1.6k
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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2.3k
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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1.2k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
18 months ago pl23 • 0
0
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1
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652
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 18 months ago by 43k • written 18 months ago by ▴ 10
2
votes
2
replies
864
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
18 months ago Manthos • 0
0
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1
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770
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 18 months ago by ★ 13k • written 18 months ago by • 0
0
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2
replies
814
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
18 months ago Ben ▴ 10
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2
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2.4k
views
MA plot for DESEq2 analysis
RNASeqData DESeq2
18 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 19 months ago by ★ 1.4k • written 19 months ago by • 0
1
vote
1
reply
906
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 19 months ago by 68k • written 19 months ago by • 0
1
vote
7
replies
1.5k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 17 months ago by 52k • written 19 months ago by • 0
0
votes
1
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828
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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Replies
Comment: Check removeBatchEffect effectiveness by Gordon Smyth 52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
Comment: DiffBind - question on the use of filtered or unfiltered input data by sloperun3az • 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash by sloperun3az • 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr by Paul Harrison ▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Votes
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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