Showing : differential gene expression • reset
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Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 12 months ago by ★ 4.6k • written 6.7 years ago by • 0
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9
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how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 6.8 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 2.6 years ago by ★ 4.6k • written 6.5 years ago by ▴ 60
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3
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Favorite plotting tweak for padj=0
deseq2 differential gene expression
updated 4.3 years ago by ★ 4.0k • written 4.3 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 4.3 years ago by ▴ 210 • written 4.3 years ago by • 0
2
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3
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Differential gene expression using DESeq2 on Ribo-Seq data
DESeq2 Ribo-Seq differential gene expression
4.4 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 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
8
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7
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Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect
updated 5.5 years ago by • 0 • written 6.3 years ago by ▴ 20
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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
5.8 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
5.8 years ago ravelarvargas • 0
3
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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 5.9 years ago by ★ 1.4k • written 5.9 years ago by • 0
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5
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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 5.9 years ago by ★ 28k • written 5.9 years ago by • 0
5
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3
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Setting gene expression thresholds for trajectory analysis using Monocle
monocle differential gene expression detectgenes function Tutorial
5.9 years ago S.Webb6 ▴ 40
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8
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4.6k
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MDS Plot help in edgeR
edgeR plotmds differential gene expression MDS mdsplot
updated 6.0 years ago by 52k • written 6.0 years ago by • 0
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3
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how to find expressed genes in RNAseq
deseq2 rnaseq differential gene expression featurecounts rnaseqGene
6.0 years ago melkile26 • 0
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5
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1.5k
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NanoStringDiff analysis with confounding factors
differential gene expression nanostring confounding factors
updated 6.0 years ago by 67k • written 6.0 years ago by • 0
3
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6
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2.5k
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Controlling numerical covariates: differential gene expression with limma voom
limma voom differential gene expression rnaseq R
updated 6.1 years ago by ▴ 280 • written 6.1 years ago by • 0
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DESeq2 estimateSizeFactors with control genes
deseq2 differential gene expression controls references
updated 6.1 years ago by ▴ 10 • written 6.1 years ago by • 0
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1.2k
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DESeq2 - shrunken log fold changes and threshold test
deseq2 lfcshrink lfcthreshold differential gene expression
updated 6.1 years ago by 43k • written 6.1 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
6.1 years ago Mithil Gaikwad • 0
2
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3
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2.1k
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Using LIMMA for differential gene analysis of microarray data
limma differential gene expression ncbi geo affymetrix microarrays
updated 6.1 years ago by ★ 28k • written 6.1 years ago by • 0
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7
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2.1k
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DESeq2 with several biological replicates
rnaseq deseq2 differential gene expression
6.1 years ago bharata1803 ▴ 60
3
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3
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1.4k
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Apply different cutoffs with edgeR pipeline and glmTreat for RNA-Seq DEG analysis
edger differential gene expression glmtreat
updated 6.1 years ago by 52k • written 6.2 years ago by ▴ 840
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3
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1.5k
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Multi-factor with interaction model in EdgeR and DESeq2
edger deseq2 rnaseq differential gene expression
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
9
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5
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Finding DE genes from RNA-seq data
edgeR pvalue qvalue fpkm differential gene expression
updated 6.2 years ago by ★ 13k • written 6.2 years ago by • 0
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898
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Multiple factor design for differential expression with DESeq2
deseq2 differential gene expression multiple factor design
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
1
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2
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1.2k
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DESEQ2 Finding Unchanged Genes
deseq2 differential gene expression
updated 6.2 years ago by 43k • written 6.2 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 6.2 years ago by 43k • written 6.2 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 6.2 years ago by ★ 1.4k • written 6.2 years ago by • 0
2
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7
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How to block for a subject in a 2 factor design formula
deseq2 differential gene expression rnaseq
6.2 years ago Onyi Ukay • 0
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2.3k
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EdgeR between unequal group sizes?
edger differential gene expression rnaseq
updated 6.2 years ago by 52k • written 6.2 years ago by ▴ 30
4
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4
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1.3k
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EdgeR blocking and "All combinations of multiple factors"
edger differential gene expression
updated 6.3 years ago by 67k • written 6.3 years ago by • 0
2
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4
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2.4k
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EdgeR analysis batch effect
edger differential gene expression
updated 6.3 years ago by ★ 28k • written 6.3 years ago by • 0
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1
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1.8k
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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 6.3 years ago by 67k • written 6.3 years ago by • 0
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7
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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 6.3 years ago by 52k • written 6.3 years ago by • 0
0
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993
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Degrees of freedom and coefficients in an edge::deSet and edge::deFit objects
edge differential gene expression timecourse interaction
6.4 years ago rubi ▴ 110
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7
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2.1k
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skewed differentially expressed gene results - DESeq2
deseq2 differential gene expression outliers
updated 6.4 years ago by ★ 7.9k • written 6.4 years ago by ▴ 20
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4
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2.1k
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Simple differential expression analysis for 2 groups
differential gene expression agilent microarrays microarray DEA Limma
6.4 years ago christiangriffioen • 0
2
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6
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2.6k
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Differentially expressed genes across multiple conditions
differential gene expression limma voom multiple treatments
updated 6.4 years ago by 67k • written 6.4 years ago by ▴ 10
3
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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 6.4 years ago by 52k • written 6.5 years ago by ▴ 120
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2
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2.6k
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What are the different strategies to filter out low count genes?
rnaseq deseq2 differential gene expression
updated 6.5 years ago by ★ 13k • written 6.5 years ago by ▴ 80
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5
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Differential analysis based on selection of random samples
r differential gene expression deseq2 bioconductor rnaseq
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 60
1
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1
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1.0k
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DeSeq2 independant filtering barely removes any genes
deseq2 differential gene expression filtering
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
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0
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1.4k
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covariate vs adjustvars
ballgown rnaseq differential gene expression tuxedo
6.5 years ago justinjj ▴ 10
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1
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886
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PROBLEM WHILE IMPORTING FOR edgeR
differential gene expression edger
6.5 years ago prakashpandey1111 • 0
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1.0k
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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 6.5 years ago by 52k • written 6.5 years ago by • 0
1
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1
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1.9k
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non-integer counts in DESeq2
deseq2 differential gene expression
updated 6.5 years ago by 43k • written 6.5 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 6.5 years ago by 52k • written 6.5 years ago by • 0
0
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0
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1.4k
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Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential gene expression differential expression
6.5 years ago manuelmendoza • 0
7
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6
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6.5k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 6.6 years ago by 52k • written 6.6 years ago by ▴ 60
50 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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