Showing : differential gene expression • reset
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Favorite plotting tweak for padj=0
deseq2 differential gene expression
updated 3.7 years ago by ★ 3.9k • written 3.7 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 3.7 years ago by ▴ 210 • written 3.7 years ago by • 0
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Differential gene expression using DESeq2 on Ribo-Seq data
DESeq2 Ribo-Seq differential gene expression
3.8 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 4.1 years ago by ★ 28k • written 4.1 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
5.2 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
5.2 years ago ravelarvargas • 0
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How to find Top 10 expressed genes in DESeq2
deseq2 baseMean differential gene expression rnaseqgene
updated 5.3 years ago by ★ 1.3k • written 5.3 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 5.3 years ago by ★ 28k • written 5.3 years ago by • 0
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Setting gene expression thresholds for trajectory analysis using Monocle
monocle differential gene expression detectgenes function Tutorial
5.3 years ago S.Webb6 ▴ 40
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MDS Plot help in edgeR
edgeR plotmds differential gene expression MDS mdsplot
updated 5.3 years ago by 50k • written 5.3 years ago by • 0
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how to find expressed genes in RNAseq
deseq2 rnaseq differential gene expression featurecounts rnaseqGene
5.4 years ago melkile26 • 0
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NanoStringDiff analysis with confounding factors
differential gene expression nanostring confounding factors
updated 5.4 years ago by 65k • written 5.4 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 5.4 years ago by ▴ 270 • written 5.4 years ago by • 0
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DESeq2 estimateSizeFactors with control genes
deseq2 differential gene expression controls references
updated 5.4 years ago by • 0 • written 5.4 years ago by • 0
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DESeq2 - shrunken log fold changes and threshold test
deseq2 lfcshrink lfcthreshold differential gene expression
updated 5.5 years ago by 42k • written 5.5 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
5.5 years ago Mithil Gaikwad • 0
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3
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Using LIMMA for differential gene analysis of microarray data
limma differential gene expression ncbi geo affymetrix microarrays
updated 5.5 years ago by ★ 28k • written 5.5 years ago by • 0
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DESeq2 with several biological replicates
rnaseq deseq2 differential gene expression
5.5 years ago bharata1803 ▴ 60
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Multi-factor with interaction model in EdgeR and DESeq2
edger deseq2 rnaseq differential gene expression
updated 5.5 years ago by 42k • written 5.5 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 5.5 years ago by 50k • written 5.5 years ago by ▴ 830
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Finding DE genes from RNA-seq data
edgeR pvalue qvalue fpkm differential gene expression
updated 5.5 years ago by ★ 13k • written 5.5 years ago by • 0
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Multiple factor design for differential expression with DESeq2
deseq2 differential gene expression multiple factor design
updated 5.5 years ago by 42k • written 5.6 years ago by • 0
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DESEQ2 Finding Unchanged Genes
deseq2 differential gene expression
updated 5.6 years ago by 42k • written 5.6 years ago by ▴ 20
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1.6k
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How to set up appropriate analysis using sample type and condition for DESeq2
deseq2 differential gene expression design
updated 5.6 years ago by 42k • written 5.6 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 5.6 years ago by ★ 1.3k • written 5.6 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
5.6 years ago Onyi Ukay • 0
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EdgeR between unequal group sizes?
edger differential gene expression rnaseq
updated 5.6 years ago by 50k • written 5.6 years ago by ▴ 30
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EdgeR blocking and "All combinations of multiple factors"
edger differential gene expression
updated 5.7 years ago by 65k • written 5.7 years ago by • 0
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2.1k
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EdgeR analysis batch effect
edger differential gene expression
updated 5.7 years ago by ★ 28k • written 5.7 years ago by • 0
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Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect
updated 4.9 years ago by • 0 • written 5.7 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 5.7 years ago by 65k • written 5.7 years ago by • 0
1
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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 5.7 years ago by 50k • written 5.7 years ago by • 0
0
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863
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Degrees of freedom and coefficients in an edge::deSet and edge::deFit objects
edge differential gene expression timecourse interaction
5.7 years ago rubi ▴ 110
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1.7k
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skewed differentially expressed gene results - DESeq2
deseq2 differential gene expression outliers
updated 5.8 years ago by ★ 7.9k • written 5.8 years ago by ▴ 20
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1.8k
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Simple differential expression analysis for 2 groups
differential gene expression agilent microarrays microarray DEA Limma
5.8 years ago christiangriffioen • 0
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Differentially expressed genes across multiple conditions
differential gene expression limma voom multiple treatments
updated 5.8 years ago by 65k • written 5.8 years ago by • 0
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Possible ways to select differential expressed genes using DeSeq2 or edgeR
R deseq2 edger differential gene expression fold change
updated 2.0 years ago by ★ 4.1k • written 5.8 years ago by ▴ 60
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8
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EdgeR for differential analysis between two cell lines without replication
edger differential gene expression rnaseq
updated 5.8 years ago by 50k • written 5.8 years ago by ▴ 110
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2
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2.2k
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What are the different strategies to filter out low count genes?
rnaseq deseq2 differential gene expression
updated 5.8 years ago by ★ 13k • written 5.8 years ago by ▴ 80
1
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1
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840
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DeSeq2 independant filtering barely removes any genes
deseq2 differential gene expression filtering
updated 5.8 years ago by 42k • written 5.9 years ago by • 0
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770
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PROBLEM WHILE IMPORTING FOR edgeR
differential gene expression edger
5.9 years ago prakashpandey1111 • 0
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1.1k
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Differential analysis based on selection of random samples
r differential gene expression deseq2 bioconductor rnaseq
updated 5.8 years ago by 42k • written 5.9 years ago by ▴ 60
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covariate vs adjustvars
ballgown rnaseq differential gene expression tuxedo
5.9 years ago justinjj ▴ 10
2
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1
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866
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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 5.9 years ago by 50k • written 5.9 years ago by • 0
1
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1
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1.7k
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non-integer counts in DESeq2
deseq2 differential gene expression
updated 5.9 years ago by 42k • written 5.9 years ago by • 0
0
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2
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1.6k
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Removing batch effect from gene expression before Limma linear modelling
Limma differential gene expression batch effect correction covariates
updated 5.9 years ago by 50k • written 5.9 years ago by • 0
0
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0
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1.2k
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Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential gene expression differential expression
5.9 years ago manuelmendoza • 0
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6
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5.8k
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scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 5.9 years ago by 50k • written 5.9 years ago by ▴ 60
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4
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2.7k
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Why DESeq2 and edgeR give different results?
deseq2 rnaseq differential gene expression edger
updated 2.9 years ago by 50k • written 6.0 years ago by ▴ 110
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1.7k
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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 6.0 years ago by 50k • written 6.0 years ago by • 0
50 results • Page 1 of 1
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
That ll be helpful. Thank you.
Comment: Log-cpm values from limma by Shaimaa Gamal • 0
I have performed RUVg correction and extracted W, factors of unwanted variation. According to limma guide, > In the limma approach to RNA…
Comment: DSS CpG coverage threshold by j.gilbert • 0
Might be a bit late for the original poster :') but in case anyone else is wondering, the DSS user guide says: *Q: Do I need to filter out…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Segmentation is of the whole genome, I'll write some code for doing this later today.
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
I'll take a look later. For next time, I've edited your post by enclosing the code in triple backticks (on their own link). This properly …
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