Showing : RNASeqData • reset
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3
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 28 days ago by 43k • written 4 weeks ago by • 0
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0
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108
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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
7 weeks ago cftattersfield • 0
0
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5
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358
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 8 weeks ago by • 0
0
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1
reply
200
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Correlation between gene clusters
genomes RNASeqData
written 10 weeks ago by • 0
0
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2
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344
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Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
10 weeks ago gingergeiger22 • 0
2
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1
reply
414
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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 12 weeks ago by • 0
0
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1
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255
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combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 12 weeks ago by • 0 • written 12 weeks ago by • 0
2
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1
reply
413
views
DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 3 months ago by 43k • written 3 months ago by • 0
0
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4
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767
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
4 months ago Philippine • 0
0
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2
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456
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 5 months ago by • 0
3
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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
554
views
WGCNA
DEGselection RNASeqData WGCNA
updated 5 months ago by ▴ 760 • written 5 months ago by • 0
1
vote
1
reply
351
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 5 months ago by ★ 4.7k • written 5 months ago by • 0
1
vote
1
reply
574
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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2.0k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 6 months ago by • 0
1
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2
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430
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Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
6 months ago Gordon • 0
0
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3
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688
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 ★ 4.7k • written 8 months ago by • 0
0
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4
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738
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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
vote
3
replies
715
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
457
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
462
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
469
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 10 months ago by 52k • written 10 months ago by • 0
0
votes
1
reply
424
views
Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 11 months ago by 68k • written 11 months ago by • 0
3
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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
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601
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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 22 months ago by • 0
1
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3
replies
859
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
13 months ago island • 0
0
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2
replies
603
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
14 months ago Diana • 0
0
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1
reply
890
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 14 months ago by ★ 4.7k • written 14 months ago by • 0
5
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6
replies
1.2k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
14 months ago Shaimaa Gamal • 0
1
vote
1
reply
754
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 15 months ago by ★ 4.7k • written 15 months ago by • 0
0
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2
replies
889
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
vote
2
replies
894
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
15 months ago drewhaydensteele • 0
1
vote
1
reply
749
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 15 months ago by ★ 4.7k • written 15 months ago by • 0
1
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2
replies
1.4k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
15 months ago Levi • 0
0
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3
replies
2.1k
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
15 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
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1
reply
623
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
811
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
votes
1
reply
735
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
776
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
16 months ago Ben ▴ 10
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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
2.1k
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
862
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
reply
777
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
0
votes
4
replies
1.2k
views
filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 18 months ago by 68k • written 18 months ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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