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2
votes
1
answer
137
views
1
answer
EdgeR for differential analysis between two cell lines without replication
rnaseq edger differential gene expression written 5 days ago by Biologist • 70 • updated 4 days ago by Gordon Smyth ♦ 34k
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2
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59
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2
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What are the different strategies to filter out low count genes?
rnaseq deseq2 differential gene expression written 6 days ago by ag1805x • 0 • updated 4 days ago by Wolfgang Huber ♦ 13k
5
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1
answer
131
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1
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Possible ways to select differential expressed genes using DeSeq2 or edgeR
edger deseq2 R differential gene expression fold change written 5 days ago by Beginner • 50 • updated 5 days ago by Axel Klenk • 910
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1
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85
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1
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Differential analysis based on selection of random samples
rnaseq deseq2 R bioconductor differential gene expression written 12 days ago by Beginner • 50 • updated 11 days ago by Michael Love ♦ 18k
1
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1
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47
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1
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DeSeq2 independant filtering barely removes any genes
deseq2 differential gene expression filtering written 12 days ago by mnaymik • 0 • updated 11 days ago by Michael Love ♦ 18k
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0
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59
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0
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covariate vs adjustvars
rnaseq differential gene expression ballgown tuxedo written 15 days ago by justinjj • 10
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0
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47
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PROBLEM WHILE IMPORTING FOR edgeR
edger differential gene expression written 12 days ago by prakashpandey1111 • 0
2
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1
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57
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1
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Differential analysis between 2 groups (n=1) vs (n=3) moderated t-test
limma differential gene expression moderated t-test small sample size written 16 days ago by mrupji • 0 • updated 16 days ago by Gordon Smyth ♦ 34k
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1
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53
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1
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non-integer counts in DESeq2
deseq2 differential gene expression written 26 days ago by warrena • 0 • updated 26 days ago by Michael Love ♦ 18k
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1
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90
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1
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Removing batch effect from gene expression before Limma linear modelling
limma differential gene expression covariates batch effect correction written 5 weeks ago by abelsousa • 0 • updated 5 weeks ago by Gordon Smyth ♦ 34k
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0
answers
61
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0
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Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential expression differential gene expression written 5 weeks ago by manuelmendoza • 0
6
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2
answers
124
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2
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scaling data for clustering heat map
rnaseq clustering edger differential gene expression heatmap written 6 weeks ago by Beginner • 50 • updated 6 weeks ago by Gordon Smyth ♦ 34k
5
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2
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174
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2
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Why DESeq2 and edgeR give different results?
rnaseq edger deseq2 differential gene expression written 7 weeks ago by Biologist • 70 • updated 7 weeks ago by Gordon Smyth ♦ 34k
4
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1
answer
128
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1
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edgeR: How can I determine which factors significantly explain my DE genes?
edger differential gene expression design matrix model.matrix written 7 weeks ago by grabear • 0 • updated 7 weeks ago by Gordon Smyth ♦ 34k
4
votes
2
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231
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Filtering step for differential analysis in edgeR
edger R bioconductor differential gene expression filtering written 9 weeks ago by Biologist • 70 • updated 9 weeks ago by Gordon Smyth ♦ 34k
0
votes
1
answer
184
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1
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TPM data Differential expression analysis
limma edger differential gene expression written 10 weeks ago by ghmdsr • 0 • updated 10 weeks ago by Gordon Smyth ♦ 34k
1
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1
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118
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1
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Differentially expressed genes detection between three classes with a batch effect in DESeq2
deseq2 differential gene expression batch effect written 11 weeks ago by francesco.tabaro • 0 • updated 11 weeks ago by Michael Love ♦ 18k
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1
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66
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1
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Global Trend Analysis using results from EdgeR
clustering edger consensusclusterplus differential gene expression kmeans written 11 weeks ago by anupriya.dalmia • 0 • updated 11 weeks ago by Aaron Lun • 20k
2
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1
answer
98
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1
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Interpretation of cngeneson when doing differential expression analysis in MAST
differential gene expression mast written 11 weeks ago by francesco.brundu@gmail.com • 40 • updated 11 weeks ago by Andrew_McDavid • 130
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73
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Human genes correlation to Bacterial genes
differential gene expression rna-seq correlation pearsoncorrelation written 12 weeks ago by saad_k6 • 0
0
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0
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82
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0
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Pipeline for Lexogen Quantseq 3' UTR Sequencing
differential gene expression rna seq lexogen quantseq written 12 weeks ago by pbachali • 0
4
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2
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117
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2
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Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
edger differential gene expression upregulated genes downregulated genes written 3 months ago by fawazfebin • 30 • updated 3 months ago by lisacarlon25 • 0
1
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1
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127
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1
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Trying to simplify Interaction analysis with edger, and propably failing to do so?
rnaseq edger interactions differential gene expression multiple factor design written 3 months ago by David Rengel • 70
1
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1
answer
137
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1
answer
DESeq2 confounding cartridge
rnaseq deseq2 differential gene expression nanostring confounders written 3 months ago by kim.malek88 • 0 • updated 3 months ago by Michael Love ♦ 18k
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1.7k
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2
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Going crazy with normalizing TCGA raw rsem gene count
rnaseq normalization cancer differential gene expression tcga written 3.2 years ago by ezz • 0 • updated 3 months ago by Dimitris Vavoulis • 0
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