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5
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DESeq2 w. pathway/network info as a prior knowledge
deseq2 pathway differential expression written 6 days ago by guidobarzaghi • 20 • updated 1 day ago by Michael Love ♦ 22k
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Using PEER to identify hidden confounders in RNA-seq data (not working)
differential expression rna-seq peer hidden confounders written 27 days ago by rodrigo.duarte88 • 0 • updated 27 days ago by Martin Morgan ♦♦ 22k
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How to handle replicates and treatment conditions in TissueEnrich package
differential expression rna-seq tissueenrich tissue-specific expression written 5 weeks ago by andrew.oler • 0 • updated 5 weeks ago by Ashish Jain • 0
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PLAGE method fails in GSVA if an overlap between gene sets and genes in expressions is less than two
gsva differential expression gene set enrichment plage written 6 weeks ago by krassowski.michal • 0
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Get the countsFromAbundance as limma input
limma deseq2 differential expression tximport written 5 months ago by Darklings • 0 • updated 5 months ago by Gordon Smyth ♦ 36k
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ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like they should be markers
deseq2 differential expression rna-seq single cell zinb-wave written 6 months ago by rory.kirchner • 60 • updated 6 months ago by Michael Love ♦ 22k
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Global expression shift using RUVSeq
rnaseq normalization ruvseq differential expression written 7 months ago by Leon • 0 • updated 7 months ago by davide risso • 810
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venDiagram after limma showing more genes after specifying up or down regulated specifically
microarray limma venn diagram differential expression venndiagram written 7 months ago by A • 40 • updated 7 months ago by James W. MacDonald ♦ 49k
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DE analysis when large portion of transcriptome is changed
edger ebseq differential expression rna-seq written 7 months ago by marhabaie • 0 • updated 7 months ago by Aaron Lun • 22k
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Deseq2 problem visualizing gene expression with batch corrected values
visualization limma deseq2 differential expression written 8 months ago by Mbosio85 • 0 • updated 8 months ago by Michael Love ♦ 22k
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DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcthreshold lfcshrink written 8 months ago by emi.sch • 10 • updated 8 months ago by Michael Love ♦ 22k
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DE analysis of orthologs with varying sequence lengths using RSEM+tximport+DEseq2: normalization for sequence length?
deseq2 differential expression tximport rsem sequence length normalization written 8 months ago by al-ash • 20 • updated 8 months ago by Michael Love ♦ 22k
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pair wise ballgown
differential expression ballgown written 8 months ago by zoe.ward • 0
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Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential expression differential gene expression written 8 months ago by manuelmendoza • 0
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differential expression analysis with big dataset and >500 surrogate variables
sva deseq2 differential expression lrt written 9 months ago by aec • 40
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244
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Interpretation of p-value plot
limma differential expression p values written 9 months ago by karlien.springael • 0 • updated 9 months ago by Gordon Smyth ♦ 36k
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Finding genes respond differently to treatment between many genotype comparison
edger differential expression nested design written 9 months ago by chiayi • 0 • updated 9 months ago by Gordon Smyth ♦ 36k
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interaction model deseq2 specific DE genes
deseq2 differential expression interaction model written 10 months ago by aec • 40 • updated 10 months ago by Michael Love ♦ 22k
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Fitting Gamma GLMs for examining differential expression
edger deseq2 differential expression written 11 months ago by jspmccain • 10 • updated 11 months ago by Ryan C. Thompson ♦ 7.2k
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Justification for collapsing technical replicates in DESeq2
rnaseq deseq2 differential expression replicate written 2.6 years ago by kieranrcampbell • 30 • updated 11 months ago by jovel_juan • 10
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457
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Analysis of pathways using edgeR
rnaseq edger kegg differential expression written 11 months ago by fawazfebin • 30 • updated 11 months ago by Gordon Smyth ♦ 36k
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How to perform time-course differential expression with "erroneous" baseline in edgeR?
timecourse edger differential expression written 12 months ago by Enzo Castillejos • 0 • updated 12 months ago by Gordon Smyth ♦ 36k
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Using DESeq2 to analyse TCGA data
deseq2 differential expression tcga gene expression tcgabiolinks written 12 months ago by victor.ramos.usp • 0 • updated 12 months ago by Michael Love ♦ 22k
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2
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Differential expressiong with two groups in BASiCS
bayesian differential expression single-cell basics written 12 months ago by muad.abdelhay • 10 • updated 12 months ago by CataVallejos • 10
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Run tweeDEseq on Flux-capacitor RPKM values
tweedeseq differential expression written 12 months ago by vrehaman • 0 • updated 12 months ago by Robert Castelo • 2.3k
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