Showing : differential gene expression • reset
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Favorite plotting tweak for padj=0
deseq2 differential gene expression
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by ▴ 20
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Error loading sample and control data using Ballgown due to different i_id in i_data.ctab
ballgown i_data.ctab differential gene expression
updated 4.5 years ago by ▴ 210 • written 4.5 years ago by • 0
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Differential gene expression using DESeq2 on Ribo-Seq data
DESeq2 Ribo-Seq differential gene expression
4.7 years ago DataFanatic ▴ 10
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Multi-level experiment with continuous varibles and confounders in limma
limma de differential gene expression multi-tissue design multi-level design
updated 5.0 years ago by ★ 28k • written 5.0 years ago by • 0
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I am trying to recreate results from an Alzheimer's paper but I can't figure out my linear regression model
limma microarray differential gene expression linear regression edger
6.1 years ago ravelarvargas • 0
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I am having trouble recreating the linear regression results published in an Alzheimer's paper
limma edger linear regression microarray differential gene expression
6.1 years ago ravelarvargas • 0
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5
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How to find Top 10 expressed genes in DESeq2
deseq2 baseMean differential gene expression rnaseqgene
updated 6.1 years ago by ★ 1.4k • written 6.1 years ago by • 0
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My linear regression model is giving me too many differentially expressed genes
limma rna-seq differential gene expression edger linear regression
updated 6.2 years ago by ★ 28k • written 6.2 years ago by • 0
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Setting gene expression thresholds for trajectory analysis using Monocle
monocle differential gene expression detectgenes function Tutorial
6.2 years ago S.Webb6 ▴ 40
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MDS Plot help in edgeR
edgeR plotmds differential gene expression MDS mdsplot
updated 6.2 years ago by 52k • written 6.2 years ago by • 0
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how to find expressed genes in RNAseq
deseq2 rnaseq differential gene expression featurecounts rnaseqGene
6.3 years ago • updated 6.2 years ago melkile26 • 0
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NanoStringDiff analysis with confounding factors
differential gene expression nanostring confounding factors
updated 6.3 years ago by 68k • written 6.3 years ago by • 0
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Controlling numerical covariates: differential gene expression with limma voom
limma voom differential gene expression rnaseq R
updated 6.3 years ago by ▴ 280 • written 6.3 years ago by • 0
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DESeq2 estimateSizeFactors with control genes
deseq2 differential gene expression controls references
updated 3 days ago by • 0 • written 6.3 years ago by • 0
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DESeq2 - shrunken log fold changes and threshold test
deseq2 lfcshrink lfcthreshold differential gene expression
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
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Error while loading the data structrure in the ballgown tool
ballgown rnaseq differential gene expression new tuxedo pipleine
6.4 years ago Mithil Gaikwad • 0
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Using LIMMA for differential gene analysis of microarray data
limma differential gene expression ncbi geo affymetrix microarrays
updated 6.4 years ago by ★ 28k • written 6.4 years ago by • 0
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DESeq2 with several biological replicates
rnaseq deseq2 differential gene expression
6.4 years ago bharata1803 ▴ 60
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Multi-factor with interaction model in EdgeR and DESeq2
edger deseq2 rnaseq differential gene expression
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
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Apply different cutoffs with edgeR pipeline and glmTreat for RNA-Seq DEG analysis
edger differential gene expression glmtreat
updated 6.4 years ago by 52k • written 6.4 years ago by ▴ 840
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Finding DE genes from RNA-seq data
edgeR pvalue qvalue fpkm differential gene expression
updated 6.4 years ago by ★ 13k • written 6.4 years ago by • 0
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Multiple factor design for differential expression with DESeq2
deseq2 differential gene expression multiple factor design
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
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DESEQ2 Finding Unchanged Genes
deseq2 differential gene expression
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 20
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6
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How to set up appropriate analysis using sample type and condition for DESeq2
deseq2 differential gene expression design
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
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deseq2 analysis multiple factor and 4 different time points
edger and deseq2 differential gene expression bias
updated 6.5 years ago by ★ 1.4k • written 6.5 years ago by • 0
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How to block for a subject in a 2 factor design formula
deseq2 differential gene expression rnaseq
6.5 years ago Onyi Ukay • 0
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EdgeR between unequal group sizes?
edger differential gene expression rnaseq
updated 6.5 years ago by 52k • written 6.5 years ago by ▴ 30
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EdgeR blocking and "All combinations of multiple factors"
edger differential gene expression
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
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EdgeR analysis batch effect
edger differential gene expression
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
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Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect
updated 5.8 years ago by • 0 • written 6.5 years ago by ▴ 20
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Combining biological replicates from raw counts for use in differential gene expression/normalization (DESeq2 and edgeR)
differential gene expression biologicalreplicates raw_counts
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
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How do I discern if a magnitude difference in expression is up-regulation in one group or down-regulation in another?
edgeR R differential gene expression up-regulation gene list
updated 6.6 years ago by 52k • written 6.6 years ago by • 0
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Degrees of freedom and coefficients in an edge::deSet and edge::deFit objects
edge differential gene expression timecourse interaction
6.6 years ago rubi ▴ 110
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skewed differentially expressed gene results - DESeq2
deseq2 differential gene expression outliers
updated 6.6 years ago by ★ 7.9k • written 6.6 years ago by ▴ 20
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Simple differential expression analysis for 2 groups
differential gene expression agilent microarrays microarray DEA Limma
6.7 years ago christiangriffioen • 0
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Differentially expressed genes across multiple conditions
differential gene expression limma voom multiple treatments
updated 6.7 years ago by 68k • written 6.7 years ago by ▴ 10
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Possible ways to select differential expressed genes using DeSeq2 or edgeR
R deseq2 edger differential gene expression fold change
updated 2.9 years ago by ★ 4.8k • written 6.7 years ago by ▴ 60
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EdgeR for differential analysis between two cell lines without replication
edger differential gene expression rnaseq
updated 6.7 years ago by 52k • written 6.7 years ago by ▴ 120
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What are the different strategies to filter out low count genes?
rnaseq deseq2 differential gene expression
updated 6.7 years ago by ★ 13k • written 6.7 years ago by ▴ 80
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DeSeq2 independant filtering barely removes any genes
deseq2 differential gene expression filtering
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
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PROBLEM WHILE IMPORTING FOR edgeR
differential gene expression edger
6.7 years ago prakashpandey1111 • 0
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Differential analysis based on selection of random samples
r differential gene expression deseq2 bioconductor rnaseq
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 60
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covariate vs adjustvars
ballgown rnaseq differential gene expression tuxedo
6.7 years ago justinjj ▴ 10
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1.1k
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Differential analysis between 2 groups (n=1) vs (n=3) moderated t-test
moderated t-test limma differential gene expression small sample size
updated 6.7 years ago by 52k • written 6.7 years ago by • 0
1
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non-integer counts in DESeq2
deseq2 differential gene expression
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
0
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2
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1.9k
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Removing batch effect from gene expression before Limma linear modelling
Limma differential gene expression batch effect correction covariates
updated 6.8 years ago by 52k • written 6.8 years ago by • 0
0
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0
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Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential gene expression differential expression
6.8 years ago manuelmendoza • 0
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scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 6.8 years ago by 52k • written 6.8 years ago by ▴ 60
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4
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Why DESeq2 and edgeR give different results?
deseq2 rnaseq differential gene expression edger
updated 3.8 years ago by 52k • written 6.8 years ago by ▴ 120
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edgeR: How can I determine which factors significantly explain my DE genes?
edger differential gene expression model.matrix design matrix
updated 6.8 years ago by 52k • written 6.8 years ago by • 0
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Comment: Annotation package for Manduca sexta by GA ▴ 10
Thank you!
Comment: Improving performance of edgeR and limma while adjusting for multiple confounder by ATpoint ★ 4.8k
If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k
We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…
Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k
It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…
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Answer: Explannation for ROAST results
A: How DiffBind run PCA based on peak data?
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
A: Is logFC a log2 fold change or some other base in scran::findMarkers
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