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<prev • 274 results • page 1 of 10 • next >
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edgeR: how to make contrasts with makeContrasts
ngs makecontrasts glm edger dge written 2 days ago by m93 • 100
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14 follow
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How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene limma edger written 11 months ago by Mike • 1.1k • updated 6 days ago by enxxx23 • 190
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138
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Making a table of RNA seq results
R rna-seq edger written 10 days ago by tw617 • 20 • updated 9 days ago by zx8754 ♦ 5.6k
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110
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How to make a gene expression correlation graph?
R rna-seq edger written 12 days ago by unawaz • 10 • updated 12 days ago by h.mon ♦ 21k
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How to identify differential expressed genes if the normalization assumptions are violated
deseq2 edger written 16 days ago by afli • 140 • updated 16 days ago by Devon Ryan ♦ 86k
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No replicates in 1 group, which idea is the best to apply?
no replicates deseq2 rna-seq edger written 23 days ago by Batu • 110 • updated 23 days ago by EagleEye ♦ 5.9k
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Should I remove samples after normalization of miRNA seq read counts ?
rna-seq edger mirnas written 9 months ago by Björn • 30 • updated 28 days ago by Biostar ♦♦ 20
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How to make cluster from gene read count?
R deseq2 rna-seq clustering edger written 5 weeks ago by ahmad mousavi • 150 • updated 29 days ago by Chirag Parsania • 1.2k
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DE Gene List to Regulatory Network
R de edger gene regulatory network written 5 weeks ago by gtasource • 20
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Is logCPM expression data good for plottinng?
plotting R geneexpression rna-seq edger written 5 weeks ago by Biologist • 90
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263
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Advice on running a differential expression analysis on patients with slightly different mutations within each group
deseq2 rna-seq differential expression edger written 6 weeks ago by unawaz • 10
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1
answer
181
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1
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design matrix for time point comparision [1 treatment] in time course RNA Seq - EdgeR
rna-seq edger masigpro written 8 weeks ago by thindmarsmission • 0 • updated 6 weeks ago by Antonio R. Franco • 3.9k
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141
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How to create design matrix for confounder (here sunlight) in edgeR ?
rnaseq edger written 6 weeks ago by Björn • 30 • updated 6 weeks ago by b.nota ♦ 5.3k
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Gene set enrichment analysis with edgeR output
R edger genesetenrichment gsea rna-seq written 7 weeks ago by Biologist • 90 • updated 7 weeks ago by h.mon ♦ 21k
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2
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TMM.normalized.FPKM vs .TMM.EXPR.matrix for populating SQL
trinity fpkm tpm sql edger written 2.1 years ago by ando.kelli • 30 • updated 7 weeks ago by egtabilin • 0
3
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Does FDR value change based Fold change cutoff?
R differential expression rna-seq edger statistics written 4 months ago by Biologist • 90 • updated 7 weeks ago by RamRS ♦ 19k
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1
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Error with combining samples into matrix using abundance_estimates_to_matrix.pl
matrix de edger rna-seq written 2.7 years ago by nikelle.petrillo • 80 • updated 7 weeks ago by RamRS ♦ 19k
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1
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Fit GLM using part of the data
scrna-seq glm edger written 8 weeks ago by rasmus.agren • 0 • updated 7 weeks ago by Kevin Blighe ♦ 32k
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167
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Problem with low count removal in edgeR ?
edger differential expression mirna written 8 weeks ago by Björn • 30
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5 follow
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How to create PCA plot and heatmaps using only significant genes in edgeR ?
R pca edger heatmaps written 4 months ago by Björn • 30 • updated 9 weeks ago by zx8754 ♦ 5.6k
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edgeR DE; choosing right coefficient from design matrix with many covariates
rna-seq edger written 9 weeks ago by Cece • 0
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180
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Error while doing EdgeR fro miRNA Seq analysis
mirnaseq tool edger written 9 weeks ago by nivya.james2016 • 0
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1
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231
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1
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RNA-seq unbalanced batch effect correction
R rna-seq edger batch effect written 10 weeks ago by sckinta • 480 • updated 10 weeks ago by Devon Ryan ♦ 86k
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179
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1
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problem in matrix generation after abundance estimation by RSEM?
rsem edger written 11 weeks ago by majeedaasim • 20 • updated 10 weeks ago by h.mon ♦ 21k
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5 follow
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News: sharing BiocWorkshops 2018
deseq2 rna-seq news limma glimma edger written 11 weeks ago by Bogdan • 680 • updated 11 weeks ago by Pierre Lindenbaum ♦ 114k
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1
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388
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1
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Why DE genes are not among highly variable genes between groups
variance edger mirna written 6 months ago by Björn • 30 • updated 11 weeks ago by Biostar ♦♦ 20
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163
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1
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Can limma/other DE algorithms be used for differential analysis of chemical descriptors?
differential analysis cheminformatics limma edger written 11 weeks ago by Alonzo • 10 • updated 11 weeks ago by Devon Ryan ♦ 86k
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making matrix model for samples with one wild type and 4 different results
R edger rna-seq deg voom written 3 months ago by moru_all • 0 • updated 3 months ago by Marks • 40
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249
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DESeq2 question: how to identify genes expressed only in one condition
R deseq2 rna-seq edger written 3 months ago by EVWS • 20 • updated 3 months ago by Kevin Blighe ♦ 32k
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How to extract normalized matrix after using calcNormFact function (with TMM method) ? edgeR
R edger rna-seq written 3 months ago by Katerina • 0 • updated 3 months ago by h.mon ♦ 21k
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