Showing : gene expression • reset
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DESeq2 # of up-and down-regulated genes are approximately equal
deseq2 gene expression
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
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4
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1.3k
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GOexpress - Error when plotting expression data
RNA-seq transcriptomics gene ontology gene expression GOexpress
updated 5.0 years ago by ▴ 350 • written 5.0 years ago by • 0
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Normalisation of Data before loading in TMixClust
rna-seq tmixclust k-means clustering gene expression genesis
5.1 years ago astridite • 0
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Job: Bioinformatics PhD: The circadian clock in the ageing plant, University of York, UK
transcriptomics gene expression time series plant biology circadian Job
5.3 years ago dezer ▴ 10
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2
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1.1k
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NanoStringDiff correction for variation between patient
NanoStringDiff GLM Gene expression
updated 5.4 years ago by 67k • written 5.4 years ago by • 0
3
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3
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2.1k
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Differential Expression Analysis in edgeR using Anova
edger anova gene expression Dispersion
updated 5.6 years ago by • 0 • written 6.0 years ago by • 0
0
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7
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1.5k
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How to read Illumina data used in the MACQ project (GSE5350)
microarray normalization Illumina data MACQ project gene expression
updated 5.7 years ago by 52k • written 5.7 years ago by • 0
0
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3
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1.5k
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How to regress phenotype ~ gene + covars in limma?
limma gene expression microarray R
updated 5.8 years ago by 52k • written 5.8 years ago by • 0
1
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3
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2.0k
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RPM data analysis with DESeq2
deseq2 RPM gene expression
5.8 years ago ruhollah.mb • 0
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5
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2.5k
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Getting opposite log2 fold change
deseq2 gene expression log2foldchange R
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
1
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2
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772
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Microarray Analysis of Sleep Deprivation Data Experimental Design
limma gene expression r diffeential expression microarray analysis
updated 5.9 years ago by 67k • written 5.9 years ago by • 0
2
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2
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1.0k
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Limma design matrix separate channel analysis with same control
limma design matrix gene expression
updated 6.0 years ago by 52k • written 6.0 years ago by • 0
2
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3
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1.2k
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How to calculate overlap between transposable elements differentially expressed in one experiment, with those expressed in another set of samples?
gene expression enrichment RNA-seq DESeq2
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 40
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3
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2.1k
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Algorithm for between and within microarray normalisation (for meta-analysis).
microarray meta-analysis gene expression
updated 6.0 years ago by 0 • written 8.5 years ago by ▴ 70
0
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2
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2.1k
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How can I compare the expression of two genes within the same sample?
gene expression rnaseq deseq2
updated 6.1 years ago by ▴ 30 • written 6.1 years ago by • 0
0
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0
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822
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problem with DeMAND, gene expression matrix input
DeMAND gene expression
6.2 years ago chipolino • 0
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0
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1.0k
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Job: Postdoctoral Research Fellowship- reinforcement learning in biology- London
job bioinformatician job machine learning gene expression experimental design Job
6.3 years ago dezer ▴ 10
3
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4
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1.2k
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edgeR analysis of cells treated with either drug1, drug2, or a time matched control at two different time points, did I set this up correctly?
edger rnaseq gene expression bioinformatics
updated 6.4 years ago by 52k • written 6.4 years ago by • 0
3
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11
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2.9k
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Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression geoquery GSE bioconductor microarray
updated 6.4 years ago by 21k • written 6.4 years ago by ▴ 20
0
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1
reply
880
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Obtaining gene expression value for a list of genes
gene expression
updated 6.5 years ago by 52k • written 6.5 years ago by ▴ 20
2
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4
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5.4k
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WGCNA: intrepreting grey unassigned "module"?
WGCNA rnaseq gene expression co-expression network
updated 6.8 years ago by ★ 3.0k • written 6.8 years ago by ▴ 10
0
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2
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1.2k
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Question about Illuminaio
illuminaio illumina human ht-12 v4 gene expression micorarray
updated 6.9 years ago by ★ 6.6k • written 6.9 years ago by • 0
2
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1
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5.2k
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Using DESeq2 to analyse TCGA data
deseq2 tcga tcgabiolinks gene expression differential expression
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
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What is the recommended method for running WGCNA on large metatranscriptomic dataset?
wgcna transcriptome big data metagenomics gene expression
7.0 years ago jol.espinoz ▴ 40
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Interpreting Affymetrix Human Genome U133 Plus 2.0 samples
gene expression gene expression data cel affy affymatrix
7.0 years ago torgeirous • 0
9
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6
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Representative gene expression value in one condition with several replicates
rnaseq gene expression edger
updated 7.1 years ago by 52k • written 7.1 years ago by ▴ 20
0
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4
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1.5k
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limma. After running a differential expression analysis... Can you get the individual gene expression levels between individual contrasts for each of…
limma gene expression differential gene expression
7.2 years ago arfranco ▴ 130
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3
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1.6k
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Anova test on gene expression data
Anova gene expression
updated 7.2 years ago by 67k • written 7.2 years ago by • 0
0
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4
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1.6k
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Gene clusters based on gene expression across samples
kmeans gene expression clustering
7.3 years ago • updated 7.2 years ago Jane Merlevede ▴ 90
1
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Reading Illumina HT12 V4.0 Data from GEO into Lumi
lumi geoquery geo illumina human ht-12 v4 gene expression
updated 7.3 years ago by 52k • written 7.3 years ago by • 0
2
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1
reply
1.2k
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gene expression data analysis and batch effect methods
batch effect gene expression
updated 7.7 years ago by ▴ 420 • written 7.7 years ago by • 0
0
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0
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1.1k
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gene expression data analysis and batch effect methods
batch effect gene expression
7.7 years ago tati6406 • 0
1
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1
reply
7.1k
views
WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna clustering gene expression
updated 7.8 years ago by ★ 3.0k • written 7.8 years ago by ▴ 10
2
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2
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1.6k
views
SAM/siggenes: Differential gene expression analysis
SAM siggenes microarray gene expression sam
8.0 years ago Brian Smith ▴ 120
0
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2
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968
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Is there any bioc tool to predict/quantify transcription factor activation using gene expression data?
transcription factor tf activation gene regulatory network gene expression
updated 8.1 years ago by • 0 • written 8.1 years ago by • 0
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0
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1.2k
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Bach effect and PEER/RUV correction on large population
methylation gene expression sva batch effect ruv
8.1 years ago carleshf ▴ 10
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Test whether expression levels of two gene sets are significantly different
R DESeq2 gene set testing gene expression
8.2 years ago Jon Bråte ▴ 260
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1.5k
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Help needed to identify common genes among datasets
datasets genes gene expression
updated 9.4 years ago by ★ 13k • written 9.4 years ago by • 0
0
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2
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barplot with ggplot2 for gene expression
ggplot2 barplot gene expression gene expression
updated 9.5 years ago by 67k • written 9.5 years ago by ▴ 130
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Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
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Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
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