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Does FDR value change based Fold change cutoff?
R differential expression rna-seq edger statistics written 3 months ago by Biologist • 70 • updated 1 day ago by RamRS ♦ 17k
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80
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Problem with low count removal in edgeR ?
edger differential expression mirna written 4 days ago by Björn • 30
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edgeR Factorial DE Design
factorial edger differential expression written 11 days ago by hamindigoblue • 0
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155
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Combining lenient prefiltering with expression filtering of the results in a DE experiment
rna-seq limma filtering differential expression written 11 weeks ago by stefanos.bamopoulos • 30 • updated 16 days ago by Biostar ♦♦ 20
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7 follow
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Analysis with no Differentially Expressed Genes?
microarray rna-seq differential expression written 4 months ago by vitor.saldanha11 • 0 • updated 28 days ago by Biostar ♦♦ 20
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125
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Using Trinity for RNA-Seq analysis in model organisms
trinity rna-seq differential expression written 5 weeks ago by fred.s.kremer • 70 • updated 5 weeks ago by h.mon ♦ 19k
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119
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Pathway test for reversal of effect (three-condition comparison)
camera differential expression gsea rna-seq written 8 weeks ago by glocke01 • 160 • updated 7 weeks ago by assaron • 170
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Assigning Fold Change for Polyester
rna-seq differential expression fold change written 9 weeks ago by priyankamaripuri • 40 • updated 9 weeks ago by h.mon ♦ 19k
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174
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Mapping reads against a de novo assembly -- no genome available
mapping differential expression written 3 months ago by Lucila • 10
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edger model matrix design of linear model
design matrix edger differential expression written 3 months ago by teabonng • 10
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How to calculate chromosomal enrichment of differentially expressed genes
permutation rna-seq differential expression written 3.7 years ago by Sakti • 350 • updated 3 months ago by Biostar ♦♦ 20
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580
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8 follow
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ATAC-seq DE analysis
atac-seq differential expression written 3 months ago by collmerr • 10 • updated 3 months ago by trausch • 1.1k
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Differential Peak Expression in ATAC-seq data
peak calling atac-seq differential expression written 21 months ago by ccag • 30 • updated 3 months ago by phosphodiester_bond • 10
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271
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8 follow
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Plotting the expression of some genes across time points
R rna-seq differential expression written 3 months ago by jivarajivaraj • 40 • updated 3 months ago by Vijay Lakhujani ♦ 3.0k
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519
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output TMM normalized counts with edgeR
differential expression rna-seq written 3 months ago by guillaume.rbt • 450 • updated 3 months ago by James Ashmore • 2.5k
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212
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Differential co-expression analysis on TCGA transcriptomic data
mirna-seq rna-seq differential expression written 3 months ago by nazaninhoseinkhan • 270
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5 follow
1
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Differential Expression of illumina microarray data
illumina microarray differential expression music written 18 months ago by bio94 • 40 • updated 4 months ago by Biostar ♦♦ 20
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211
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1
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Differential expression analysis with DEseq2 : multiple groups comparison
rna-seq differential expression written 4 months ago by guillaume.rbt • 450 • updated 4 months ago by Devon Ryan ♦ 84k
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300
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7 follow
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rna seq replicates not clustering
pca rna-seq differential expression written 4 months ago by guillaume.rbt • 450
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517
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ATAC-seq : call peaks, reproducibility and differential analysis without replicates
atac-seq differential expression sequencing written 4 months ago by anais1396 • 20 • updated 4 months ago by i.sudbery • 2.5k
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how to consider batch effect in design matrix?
R design matrix edger differential expression written 5 months ago by star • 60
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798
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Normalization and differential analysis in ATAC-seq data
peak calling atac-seq differential expression written 5 months ago by anais1396 • 20 • updated 5 months ago by RamRS ♦ 17k
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165
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differential expression from multiple sequencing panels
limma rna-seq differential expression written 5 months ago by glocke01 • 160
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Differential expression between two biological samples sequenced with single-cell RNA-seq with thousands of cells in each
single-cell R rna-seq differential expression written 5 months ago by Naim.Mahi • 40
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RNA-seq: Explain STAR quantMode geneCounts values
star rna-seq differential expression written 23 months ago by williantafsilva • 130 • updated 5 months ago by Tao • 240
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count based or cpm based filtering for miRNA normalization when library size is small.
rnaseq mirna edger differential expression cpm written 6 months ago by Björn • 30
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469
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Deseq2 Differentially Expressed Genes between conditions
R deseq2 rna-seq differential expression gsea written 5 months ago by bryce.kirby • 0 • updated 5 months ago by Buffo • 1.1k
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Differential Expression in DEseq2 to GSEA (9 samples, 3 conditions)
stringtie deseq2 rna-seq differential expression written 5 months ago by bryce.kirby • 0 • updated 5 months ago by Kevin Blighe ♦ 28k
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429
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5 follow
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hisat2 analysis and cuffdiff
rna-seq differential expression written 6 months ago by qudrat • 50
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DESeq2 "DESeqDataSetFromMatrix" error
deseq2 rna-seq differential expression written 6 months ago by Ricky • 20
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