Showing : RNASeqR • reset
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Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 13 months ago by 40k • written 13 months ago by • 0
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3
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838
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using of z score in Differentially Expression Analysis
RNASeqR
updated 13 months ago by ★ 3.4k • written 13 months ago by • 0
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2
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1.4k
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Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 26 days ago by • 0 • written 17 months ago by • 0
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595
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edgeR for SDE analysis
RNASeqRData edgeR RNASeqR RNASeqData
updated 19 months ago by 48k • written 19 months ago by • 0
1
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3
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909
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Error with hclust
RNASeqR #hclust #wgcna #dissimilarity #average
updated 22 months ago by ★ 3.4k • written 22 months ago by • 0
4
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1.4k
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mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 23 months ago by 40k • written 23 months ago by ▴ 10
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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 23 months ago by 63k • written 23 months ago by • 0
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743
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Outliers on DESEq2 Results
RNASeqR DifferentialExpression DESeq2
updated 2.0 years ago by 40k • written 2.0 years ago by • 0
2
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2
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995
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Need help in determing upregulated and downregulated genes
RNASeqR
2.4 years ago Rishav ▴ 20
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Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
2.4 years ago dantasezequiel1 • 0
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GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
2.5 years ago hgalmoore • 0
0
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707
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Limma Voom Design and Contrast Matrix- Can my parameter also be a factor?
RNASeqRData limma RNASeq RNASeqR
updated 2.5 years ago by 48k • written 2.5 years ago by • 0
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5
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1.3k
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while designing matrix i got an error, please help me out
RNASeqR
updated 2.5 years ago by ▴ 720 • written 2.5 years ago by ▴ 20
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2
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665
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Bioconductor packages for doing tRNA seq analysis
RNASeqR
updated 2.5 years ago by 48k • written 2.5 years ago by ▴ 20
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3
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661
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Need help in doing network analysis using R
RNASeqR
updated 2.5 years ago by ★ 3.4k • written 2.5 years ago by ▴ 20
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2
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646
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Error occured in designing a matrix
RNASeqR
updated 2.5 years ago by 48k • written 2.5 years ago by ▴ 20
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2
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930
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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
2.5 years ago Rishav ▴ 20
1
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5
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669
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Error when calculating DE using the classical approach in edgeR
RNASeqR
2.5 years ago Rishav ▴ 20
0
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1
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1.6k
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Biological replicates in DESeq2
DESeq2 Bioconductor RNASeqR
updated 2.6 years ago by ★ 3.4k • written 2.6 years ago by • 0
5
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9
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2.9k
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How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 9 weeks ago by 40k • written 2.6 years ago by ▴ 40
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812
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Using tximport to create the input for DESeq2
RNASeqR
updated 2.6 years ago by 40k • written 2.6 years ago by • 0
5
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5
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1.9k
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analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO RNASeqR Transcriptomics
updated 2.6 years ago by 63k • written 2.6 years ago by ▴ 10
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3.8k
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TPM data in limma/voom
voom limma DifferentialExpression edgeR
2.6 years ago RJM • 0
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10
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2.2k
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Duplicate correlation with limma in before-after exposure experiment
RNASeqR
2.8 years ago • updated 2.4 years ago sofie.haglund • 0
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605
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Find significant genes related to a specific disease
GeneExpression RNASeqR limma
updated 2.8 years ago by ▴ 490 • written 2.8 years ago by • 0
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6
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2.7k
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WHat is the difference between DEG and TopVarGenes in DESEq2?
DESeq2 R RNASeqR
2.8 years ago ecg1g15 ▴ 20
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5
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1.4k
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Volcano plot - select additional gene
EnhancedVolcano RNASeqR R volcanoplot
updated 2.9 years ago by 3.8k • written 2.9 years ago by ▴ 10
27 results • Page 1 of 1
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Comment: LIMMA dupcor() function time issue. by Gordon Smyth 48k
That's ok, but there is nothing to be gained by subsetting 1000 times. It would be better to simply subset 100,000 rows once, although the …
Comment: Specifying evidence channels in STRINGdb by robynne.braun • 0
Also I found prior thread here addressing the same question with response that functionality will be supported someday. This was a few year…
Comment: Problems with FLOWAI by SHASHI • 0
please try this using short path name and keeping your fcs file and wsp file in your local directory https://youtu.be/xLeqE7PNYzA
Comment: DataFrame Construction With Non-standard Column by Hervé Pagès 16k
SimpleList is a List derivative and List derivatives in general don't need protection. For example, a GRangesList object (which is also a L…
Answer: Deseq2, how to model design for comparing Mutant mouse at age 14 days versus Mu by swbarnes2 ★ 1.3k
The Status grouping you show above is good to use if you want to simply compare one subset of samples to another subset. The ~Genotype +…
Votes
Answer: Deseq2, enrichGO and ensembl ID
A: LIMMA dupcor() function time issue.
A: LIMMA dupcor() function time issue.
Answer: Further analysis after limma regression output
A: collapseReplicates in DESeq2
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