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Deseq2 does not recognize htseq count outputs
deseq2 rna-seq inputs are not recognized written 1 hour ago by nazaninhoseinkhan • 190
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83
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DiffBind 4 way comparison with N=3 for each
diffbind deseq2 chip-seq written 15 hours ago by rbronste • 140
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What are the major differences in the computation of DE genes between deseq2 and limma?
R deseq2 limma differential expression rna-seq written 3 days ago by sbrown669 • 10
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GSEA following DESeq2
R deseq2 rna-seq gsea written 18 days ago by sup230 • 10 • updated 18 days ago by geek_y ♦ 7.8k
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1
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218
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DESEQ2 for ASE
allele-specific expression deseq2 rna-seq written 20 days ago by grant.hovhannisyan • 120
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Pipeline for analysing RNA-seq exon level data with lot of samples?
dexseq deseq2 diffsplice diffsplicedge rna-seq written 21 days ago by sarin.heikki.v • 10
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5 follow
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Enrichment Analysis from DESeq2 data
deseq2 rna-seq written 24 days ago by gkuffel22 • 20 • updated 24 days ago by EagleEye • 4.6k
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1
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195
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1
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RNA-Seq time course DESeq2 analysis
deseq2 time-course rna-seq written 4 weeks ago by remi.willamme • 0 • updated 4 weeks ago by Constantine • 150
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how to know in which category certain OTUs are abundant?
R ggplot2 deseq2 written 5 weeks ago by rahulbiosciences • 0 • updated 5 weeks ago by Istvan Albert ♦♦ 73k
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What the heck is going on with this DESeq2 MA Plot?
R deseq2 ma plot rna-seq written 6 weeks ago by Kristin Muench • 170
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rnaseq data vs. phenotype
tophat2 deseq2 rna-seq written 6 weeks ago by firatuyulur • 160
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5 follow
1
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Using StringTie with DESeq2(StringTie geneID and corresponding Ensembl geneID)
stringtie deseq2 written 6 weeks ago by Megan • 30 • updated 6 weeks ago by stephensmithgalway • 20
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What is an optimal normalization approach for comparing GTEx RNASeq normal vs TCGA tumor samples?
normalization sva deseq2 rna-seq written 23 months ago by Samir • 120 • updated 6 weeks ago by mforde84 • 810
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Retrieving Annotation data from runTest() created object
deseq2 topgo gene ontology rna-seq written 7 weeks ago by Sreeraj Thamban • 30
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Advice needed on RNAseq technical and biological replicates analysis using DEseq2
next-gen deseq2 rna-seq written 7 weeks ago by macmath • 110 • updated 7 weeks ago by Samuel Brady • 230
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149
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DESeq stuck at final dispersion estimates (SubmitJobs)
deseq2 rna-seq biocparallel written 7 weeks ago by mmfansler • 20
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193
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how investigate genes after meta-analysis in each experiment
deseq2 meta-analysis metaseq deg written 8 weeks ago by Edalat • 10 • updated 7 weeks ago by Biostar ♦♦ 20
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1
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236
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1
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How to perform DESeq2 based on paired sample test?
deseq2 rna-seq written 8 weeks ago by Xiaokang ZH • 20 • updated 8 weeks ago by Devon Ryan ♦ 70k
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317
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How to analyze differentially expressed lncRNA from total RNA
deseq2 rna-seq lncrna written 9 weeks ago by ta_awwad • 90 • updated 9 weeks ago by EagleEye • 4.6k
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150
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How does deseq2 encode more than 2 levels
deseq2 rna-seq differential expression written 9 weeks ago by -_- • 450
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375
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Isoform Differential Expression Analysis
ebseq deseq2 rsem rna-seq written 7 months ago by john • 30 • updated 10 weeks ago by kristoffer.vittingseerup • 210
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Add GenomicRanges to SummarizedExperiment
deseq2 summarizedexperiment granges written 7 months ago by s.w.vanderlaan • 40 • updated 10 weeks ago by WouterDeCoster ♦ 20k
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Install DESeq2 and edgeR with Anaconda
deseq2 anaconda edger written 10 weeks ago by salamandra • 70 • updated 10 weeks ago by Sean Davis ♦ 23k
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215
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7 follow
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Conflicting results with DESeq2 between versions
R deseq2 rna-seq written 10 weeks ago by BioBing • 80
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254
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DeSeq2 MA plot
maplot deseq2 rna-seq written 11 weeks ago by niu.shengyong • 10
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RNAseq - matrix design in DESeq2 or edgeR
deseq2 rna-seq edger matrix design written 12 weeks ago by xioli2013 • 0
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Tool: DEA.R: Command line script for differential expression analysis with R packages (DESeq2/edgeR/limma-voom)
limma deseq2 tool edger rna-seq written 12 months ago by WouterDeCoster ♦ 20k
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DESeq2 + de novo assembly
de novo trinity deseq2 rna-seq dge written 12 weeks ago by pablo61991 • 30 • updated 12 weeks ago by Biojl • 1.5k
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Using RPK counts as DESeq2 input
deseq2 written 3 months ago by adityabandla • 20 • updated 3 months ago by Devon Ryan ♦ 70k
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DESeq2: Find differentially expressed genes specific to one condition
deseq2 rna-seq written 2.2 years ago by Christian • 2.5k • updated 3 months ago by Martombo • 1.7k
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