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Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
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3
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1.8k
views
using of z score in Differentially Expression Analysis
RNASeqR
updated 2.3 years ago by ★ 4.5k • written 2.3 years ago by • 0
0
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2
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3.1k
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Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 15 months ago by • 0 • written 2.6 years ago by • 0
1
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1
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975
views
edgeR for SDE analysis
RNASeqRData edgeR RNASeqR RNASeqData
updated 2.8 years ago by 51k • written 2.8 years ago by • 0
1
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3
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1.4k
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Error with hclust
RNASeqR #hclust #wgcna #dissimilarity #average
updated 3.0 years ago by ★ 4.5k • written 3.0 years ago by • 0
4
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1
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2.5k
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mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 10
0
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1
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1.0k
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Question about normalizing and removing batch effects from bulk RNA-seq data from NCBI-SRA
Arabidopsis_thaliana_Data RNASeqR Normalization BatchEffect
updated 3.1 years ago by 67k • written 3.1 years ago by ▴ 20
0
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1
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1.1k
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Outliers on DESEq2 Results
RNASeqR DifferentialExpression DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
2
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2
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2.0k
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Need help in determing upregulated and downregulated genes
RNASeqR
3.6 years ago Rishav ▴ 20
1
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3
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2.2k
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Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
3.6 years ago dantasezequiel1 • 0
3
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4
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1.7k
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GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
3.7 years ago hgalmoore • 0
0
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1
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1.0k
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Limma Voom Design and Contrast Matrix- Can my parameter also be a factor?
RNASeqRData limma RNASeq RNASeqR
updated 3.7 years ago by 51k • written 3.7 years ago by • 0
1
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5
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1.8k
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while designing matrix i got an error, please help me out
RNASeqR
updated 3.7 years ago by ▴ 780 • written 3.7 years ago by ▴ 20
1
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2
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959
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Bioconductor packages for doing tRNA seq analysis
RNASeqR
updated 3.7 years ago by 51k • written 3.7 years ago by ▴ 20
1
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3
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1.1k
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Need help in doing network analysis using R
RNASeqR
updated 3.7 years ago by ★ 4.5k • written 3.7 years ago by ▴ 20
1
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2
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984
views
Error occured in designing a matrix
RNASeqR
updated 3.7 years ago by 51k • written 3.7 years ago by ▴ 20
1
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2
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1.9k
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I am creating contrast matrix and i am following every procedure but still i don't understand where i am getting error
RNASeqR
3.7 years ago Rishav ▴ 20
1
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5
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1.1k
views
Error when calculating DE using the classical approach in edgeR
RNASeqR
3.7 years ago Rishav ▴ 20
0
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1
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2.8k
views
Biological replicates in DESeq2
DESeq2 Bioconductor RNASeqR
updated 3.7 years ago by ★ 4.5k • written 3.7 years ago by • 0
6
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11
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5.0k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 8 months ago by • 0 • written 3.7 years ago by ▴ 40
0
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1
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1.2k
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Using tximport to create the input for DESeq2
RNASeqR
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
5
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5
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3.1k
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analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO RNASeqR Transcriptomics
updated 3.8 years ago by 67k • written 3.8 years ago by ▴ 10
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2
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6.6k
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TPM data in limma/voom
voom limma DifferentialExpression edgeR
3.8 years ago RJM • 0
1
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10
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3.4k
views
Duplicate correlation with limma in before-after exposure experiment
RNASeqR
4.0 years ago • updated 3.6 years ago sofie.haglund • 0
0
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1
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860
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Find significant genes related to a specific disease
GeneExpression RNASeqR limma
updated 4.0 years ago by ▴ 510 • written 4.0 years ago by • 0
7
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6
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4.1k
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WHat is the difference between DEG and TopVarGenes in DESEq2?
DESeq2 R RNASeqR
4.0 years ago ecg1g15 ▴ 30
3
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5
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2.6k
views
Volcano plot - select additional gene
EnhancedVolcano RNASeqR R volcanoplot
updated 4.1 years ago by ★ 4.0k • written 4.1 years ago by ▴ 10
27 results • Page 1 of 1
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Answer: DESeq2 sizefactors counfounded with biological treatment by James W. MacDonald 67k
Your question is off-topic for this site, which is primarily intended to help people with technical issues with Bioconductor packages rathe…
Comment: Epic v2 Annotation CpG_maf source? by Meghan • 0
Thank you, so much, for this reply!
Comment: txdb.mmusculus.ucsc.mm10.knowngene issue on X chromosome by remi-xavier.coux ▴ 10
That indeed worked, thanks a lot for the help (and for karyoploteR)
Comment: conumee with Infinium MethylationEPIC v2.0 by fraober • 0
i also have the same issue, if anyone managed to find a solution it would be great if you could share it! (EPICv2 samples + conumee2 (not c…
Comment: Conumee with EPICv2 Segment function by fraober • 0
i also have the same issue, if anyone managed to find a solution it would be great if you could share it! (EPICv2 samples + conumee2 (not c…
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Comment: txdb.mmusculus.ucsc.mm10.knowngene issue on X chromosome
Answer: Epic v2 Annotation CpG_maf source?
Answer: bioconductor packages on bioconda
Filtering low variance genes for WGCNA
A: Filtering low variance genes for WGCNA
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