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retrieve TPM matrix from raw counts matrix or DESeq2 object dds
deseq2 tpm raw counts tcga brca written 30 minutes ago by HKS • 10
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DEseq2 results differs greatly when comparing output from STAR/featureCounts and Salmon
deseq2 salmon star rna-seq written 3 hours ago by testtube • 0 • updated 1 hour ago by i.sudbery ♦ 7.7k
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DESeq2 likelihood ratio test log fold change interpretation/calculation
deseq2 rna-seq lrt written 11 hours ago by Argonaut • 0 • updated 6 hours ago by Kevin Blighe ♦ 59k
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55
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Subset DEG from Deseq2-use padj from results() or lfcShrink()?
deseq2 rna-seq written 1 day ago by s.l.lee • 0
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Help understanding Deseq2 '~group' contrasts
deseq2 de rna-seq written 4.0 years ago by mbio.kyle • 360 • updated 1 day ago by Biostar ♦♦ 20
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Complex design matrix for different comparisons between treatments and/or cell-types
differential analysis design matrix deseq2 edger written 4 days ago by tanagholattorobche • 0
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How to generate a dataframe of deseq2 result excluding 'low counts' and 'outliers' ?
deseq2 rna-seq written 5 days ago by tianshenbio • 40 • updated 4 days ago by Kevin Blighe ♦ 59k
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RNA Seq data distribution
libraries deseq2 rna seq distribution written 4 days ago by felipead66 • 50
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79
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Generating A Heatmap for specific samples.
deseq2 rna-seq heatmap written 5 days ago by fouerghi20 • 0 • updated 5 days ago by dtm2451 • 20
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DESeq2 for pairwise comparison of multiple groups
R deseq2 rna-seq written 5 days ago by thjnant • 100
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48
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Deseq2 with continous variable
deseq2 written 5 days ago by David • 160 • updated 5 days ago by Kevin Blighe ♦ 59k
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1
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91
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1
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Problem installing DESeq2 in R4.0 linux16.04
R warnings deseq2 rna-seq package written 5 days ago by matiasbmg • 0
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Sample clustering in RNASeq
rnaseq deseq2 myposts heatmap written 4.8 years ago by noushin.farnoud • 100 • updated 10 days ago by Biostar ♦♦ 20
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DESeq2/RNA-Seq: Cross-study comparisons with large control-variance?
deseq2 rna-seq edger limma written 16 days ago by Felix • 0 • updated 15 days ago by Kevin Blighe ♦ 59k
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How to get differential gene expression within paired samples using EdgeR or DESeq2?
paired samples deseq2 designmatrix rna-seq edger written 16 days ago by learner.bioinformatics • 0
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Deseq2 getting ANOVA-like result from 3 by 3 factor design
R deseq2 rna-seq anova written 17 days ago by cwwong13 • 0 • updated 17 days ago by genomax ♦ 83k
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Issues with adding gene name and entrez ID to DESeq2 result having Ensembl ID.
ensembl deseq2 rna-seq written 17 days ago by Ranan Jyoti Sarma • 60 • updated 17 days ago by Kevin Blighe ♦ 59k
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DESeq2, batch effect correction, multiple conditions
deseq2 rna-seq written 9 weeks ago by Sy80 • 0 • updated 17 days ago by Kevin Blighe ♦ 59k
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1
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970
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Pipeline for analysing RNA-seq exon level data with lot of samples?
dexseq deseq2 diffsplice diffsplicedge rna-seq written 2.8 years ago by sarin.heikki.v • 10 • updated 19 days ago by Biostar ♦♦ 20
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Difference of DiffBind library size normalisation vs DESeq2 library size normalisation
diffbind deseq2 chip-seq rna-seq normalisation written 20 days ago by bioinfouser • 50 • updated 20 days ago by Rory Stark • 660
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Deseq2 design matrix for multiple factors
design matrix deseq2 rna-seq written 21 days ago by Ankit • 130 • updated 20 days ago by ATpoint ♦ 34k
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99
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How to subset DESeq2 results
deseq2 gsea written 21 days ago by DataFanatic • 200 • updated 21 days ago by igor ♦ 10k
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Interaction Factors Removing All Variability
R deseq2 deseq rna-seq written 21 days ago by tyak9569 • 0
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Does result data after DESeq2 analysis contain normalised counts ?
R deseq2 normalisation rna-seq written 23 days ago by hariprasadp.iitkgp • 0 • updated 23 days ago by ATpoint ♦ 34k
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DESeq2 for one time-point versus two other time-points
deseq2 written 23 days ago by jkanbar • 0
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100
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Gene set enrichment analysis input data
gse deseq2 written 23 days ago by DataFanatic • 200
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102
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DESeq2 on GEO dataset
geo R preprocessing deseq2 rna-seq written 25 days ago by hariprasadp.iitkgp • 0
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How to evaluate the performance of an RNA-seq pipeline
R differentialexpression deseq2 rna-seq written 26 days ago by nickhir • 10 • updated 26 days ago by geek_y ♦ 11k
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105
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High logfold change but padj > 0.1 in DESEQ2
R deseq2 rna-seq expression written 26 days ago by thjnant • 100 • updated 26 days ago by ATpoint ♦ 34k
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7 follow
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Massive L2FC in DESeq2
deseq2 ashr rna-seq written 29 days ago by Alex • 20
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