Showing: differential expression • reset
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Scran: Performing DE after cell-typle identifaction on the corrected and integrated datasets
differential expression scran single-cell mnn_correct written 4 days ago by baldissera152 • 0
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Limma - Using removeBatchEffect before differential expression analysis
limma differential expression batch effect written 10 days ago by jmoon1194 • 0 • updated 10 days ago by James W. MacDonald ♦ 49k
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Using PEER to identify hidden confounders in RNA-seq data (not working)
differential expression rna-seq peer hidden confounders written 8 weeks ago by rodrigo.duarte88 • 0 • updated 8 weeks ago by Martin Morgan ♦♦ 23k
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How to handle replicates and treatment conditions in TissueEnrich package
differential expression rna-seq tissueenrich tissue-specific expression written 9 weeks ago by andrew.oler • 0 • updated 9 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 10 weeks ago by krassowski.michal • 0
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Get the countsFromAbundance as limma input
limma deseq2 differential expression tximport written 6 months ago by Darklings • 0 • updated 6 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 7 months ago by rory.kirchner • 60 • updated 7 months ago by Michael Love ♦ 22k
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Global expression shift using RUVSeq
rnaseq normalization ruvseq differential expression written 8 months ago by Leon • 0 • updated 8 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 8 months ago by A • 40 • updated 8 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 8 months ago by marhabaie • 0 • updated 8 months ago by Aaron Lun • 23k
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Deseq2 problem visualizing gene expression with batch corrected values
visualization limma deseq2 differential expression written 9 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 9 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 9 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 9 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 10 months ago by aec • 40
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Interpretation of p-value plot
limma differential expression p values written 10 months ago by karlien.springael • 0 • updated 10 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 10 months ago by chiayi • 0 • updated 10 months ago by Gordon Smyth ♦ 36k
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interaction model deseq2 specific DE genes
deseq2 differential expression interaction model written 11 months ago by aec • 40 • updated 11 months ago by Michael Love ♦ 22k
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Fitting Gamma GLMs for examining differential expression
edger deseq2 differential expression written 12 months ago by jspmccain • 10 • updated 12 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 12 months ago by jovel_juan • 10
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Analysis of pathways using edgeR
rnaseq edger kegg differential expression written 12 months ago by fawazfebin • 30 • updated 12 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 13 months ago by Enzo Castillejos • 0 • updated 13 months ago by Gordon Smyth ♦ 36k
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Using DESeq2 to analyse TCGA data
deseq2 differential expression tcga gene expression tcgabiolinks written 13 months ago by victor.ramos.usp • 0 • updated 13 months ago by Michael Love ♦ 22k
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Differential expressiong with two groups in BASiCS
bayesian differential expression single-cell basics written 13 months ago by muad.abdelhay • 10 • updated 13 months ago by CataVallejos • 10
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