Showing : RNASeqData • reset
3
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6
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851
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 4 weeks ago by • 0
0
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2
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468
views
After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 23 days ago by • 0 • written 3 months ago by • 0
3
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13
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2.2k
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 14 months ago by • 0
3
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2
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1.5k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 6 months ago by ▴ 20
0
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1
reply
781
views
DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
1
vote
1
reply
449
views
Merging annotation with differential expression output
annotation RNASeqData
updated 9 months ago by 68k • written 9 months ago by • 0
0
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3
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1.0k
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 10 months ago by 43k • written 10 months ago by • 0
0
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0
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369
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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
10 months ago cftattersfield • 0
0
votes
5
replies
752
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 11 months ago by • 0
0
votes
1
reply
482
views
Correlation between gene clusters
genomes RNASeqData
written 11 months ago by • 0
0
votes
2
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736
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
11 months ago gingergeiger22 • 0
2
votes
1
reply
745
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 11 months ago by 43k • written 12 months ago by • 0
0
votes
1
reply
652
views
combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 12 months ago by • 0 • written 12 months ago by • 0
2
votes
1
reply
751
views
DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 12 months ago by 43k • written 13 months ago by • 0
0
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4
replies
1.1k
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
14 months ago Philippine • 0
0
votes
2
replies
834
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 14 months ago by • 0
1
vote
1
reply
996
views
WGCNA
DEGselection RNASeqData WGCNA
updated 14 months ago by ▴ 760 • written 14 months ago by • 0
1
vote
1
reply
719
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
1
vote
1
reply
882
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 15 months ago by 53k • written 15 months ago by • 0
1
vote
2
replies
3.3k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 15 months ago by • 0
1
vote
2
replies
712
views
Questions in Regards to LFC shrinkage in DESeq2
Dseq2 RNASeqData apeglm
16 months ago Gordon • 0
0
votes
3
replies
1.0k
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
0
votes
4
replies
1.1k
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 17 months ago by • 0
1
vote
3
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2.0k
views
Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
18 months ago Tanvi • 0
1
vote
3
replies
1.1k
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 18 months ago by 68k • written 18 months ago by ▴ 50
0
votes
1
reply
660
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 18 months ago by 68k • written 18 months ago by • 0
0
votes
1
reply
752
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 15 months ago by ▴ 20 • written 19 months ago by • 0
0
votes
1
reply
664
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 20 months ago by 53k • written 20 months ago by • 0
0
votes
1
reply
678
views
Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 21 months ago by 68k • written 21 months ago by • 0
3
votes
5
replies
1.8k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 22 months ago by 43k • written 22 months ago by ▴ 10
0
votes
0
replies
779
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
22 months ago Abril • 0
1
vote
2
replies
2.5k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.6 years ago by • 0
1
vote
3
replies
1.2k
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
23 months ago island • 0
0
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2
replies
854
views
ConsensusClusterPlus dosesn't make an output file
ConsensusClusterPlus RNASeqData
23 months ago Diana • 0
0
votes
1
reply
1.2k
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
5
votes
6
replies
1.6k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
23 months ago Shaimaa Gamal • 0
1
vote
1
reply
988
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 24 months ago by ★ 5.0k • written 2.0 years ago by • 0
0
votes
2
replies
1.3k
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
2.0 years ago Luca • 0
0
votes
1
reply
1.7k
views
Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 2.0 years ago by 68k • written 2.0 years ago by • 0
1
vote
2
replies
1.2k
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
2.1 years ago drewhaydensteele • 0
1
vote
1
reply
971
views
Differential gene expression analysis
RNASeqData RNAseq123
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
1
vote
2
replies
1.9k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
2.1 years ago • updated 24 months ago Levi • 0
0
votes
3
replies
2.7k
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
2.1 years ago Oenone • 0
3
votes
4
replies
1.5k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
2.1 years ago pl23 • 0
0
votes
1
reply
803
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by ▴ 10
2
votes
2
replies
1.1k
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
2.1 years ago Manthos • 0
0
votes
1
reply
911
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 2.1 years ago by ★ 13k • written 2.1 years ago by • 0
0
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2
replies
1.0k
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
2.1 years ago Ben ▴ 10
0
votes
2
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2.7k
views
MA plot for DESEq2 analysis
RNASeqData DESeq2
2.1 years ago RHEA • 0
2
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3
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2.7k
views
Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by • 0
152 results • Page 1 of 4
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Comment: nice 3D displays for PCA analysis by adam80haynes • 0
That's a fascinating application of 3D printing in a scientific context. Using this technology to create custom lab equipment, models of mo…
Comment: Bioinformatician at the Lausanne University Hospital by TikTsokaasocissalpc • 0
The Random Word Generator in Italian is a useful tool for generating ideas and exploring new approaches, much like the innovative research …
Comment: DECIPHER DesignProbes unable to design FISH-probes by TikTsokaasocissalpc • 0
If you want to share your research progress and microbiome discoveries with colleagues or friends, [snaptroid android][1] download free mak…
Answer: Limma-voom sample weights and impact on DEG numbers by Gordon Smyth 53k
I recommend that you always use voomLmFit() instead of the earlier voom() or voomWithQualityWeights() functions. Personally, I would use sa…
Answer: wgcna module preseravtion taking too long? by ATpoint ★ 5.0k
WGCNA is not a Bioconductor package, you won't get an answer here. Consider biostars.org or the r/bioinformatics reddit. Note that 10 sampl…
Votes
Limma-voom sample weights and impact on DEG numbers
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
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