Showing : geneexpression • reset
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Reading gene expression data in GPR format and converting it to xlsx format
BiocWorkflowTools BiomedicalInformatics GeneExpression
updated 13 hours ago by 68k • written 20 hours ago by • 0
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198
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WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 6 weeks ago by ★ 4.7k • written 7 weeks ago by • 0
2
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1
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289
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Using Affymetrix Custom Array
ArrayExpress makecdfenv AffymetrixChip gcrma GeneExpression
updated 3 months ago by 68k • written 3 months ago by • 0
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327
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 3 months ago by 43k • written 3 months ago by • 0
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9
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971
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 9 months ago by ★ 4.7k • written 9 months ago by • 0
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3
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809
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"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression Clustering ctsGE
12 months ago jbgnielson • 0
2
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799
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DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
15 months ago Manthos • 0
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3
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4.0k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 17 months ago by 52k • written 18 months ago by • 0
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1
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840
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Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
19 months ago Arianna • 0
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2
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3.1k
views
FeatureCounts Output Counts at Exon Level Using Default Settings, want gene level
GeneExpression
22 months ago CDSPARKS ▴ 30
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949
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Heatmap of two conditions from the normalized gene count data
GeneExpression heatmaps
updated 2.0 years ago by ★ 4.7k • written 2.0 years ago by • 0
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1
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4.1k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 2.1 years ago by ★ 4.7k • written 2.1 years ago by • 0
3
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4
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2.4k
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Comparing different method for DESEQ2
DESeq2 GeneExpression
updated 2.4 years ago by 43k • written 2.5 years ago by • 0
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3
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1.4k
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CountOverlap
GeneExpression ChIPSeqData
updated 2.5 years ago by 68k • written 2.5 years ago by ▴ 20
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621
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Free Gibbson energy RNA doublex
GeneExpression RNAinteract
2.6 years ago Tamina • 0
1
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0
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828
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Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
2.7 years ago hlee ▴ 10
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1.2k
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Seeking help in multifactor differential gene expression analysis using DESeq2. Can not get significance difference while comparing 3 time factor (…
DifferentialExpression GeneExpression R enrichment DEGseq
updated 2.7 years ago by ★ 1.4k • written 2.7 years ago by • 0
0
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1
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823
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Error "DESeqDataSetFromMatrix" function not found
GeneExpression
updated 2.7 years ago by ▴ 780 • written 2.7 years ago by • 0
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1
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889
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Aggregate differentially expressed genes across all contrast results using DEVis
DifferentialExpression NanoporeRNASeq DESeq2 GeneExpression DEVis
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
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1
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1.0k
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Error while using champ.SVD function
GeneExpression
updated 2.9 years ago by ▴ 780 • written 2.9 years ago by • 0
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1
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2.2k
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GDCprepare of STAR - counts
GeneExpression TCGAbiolinks
updated 2.5 years ago by • 0 • written 2.9 years ago by • 0
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0
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1.1k
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Volcano plot: Putting calculated values in legend
GeneExpression
updated 2.9 years ago by ★ 4.0k • written 2.9 years ago by • 0
2
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2
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1.1k
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Could use some advice on analyzing ranks of expressed genes in two conditions,
GeneExpression DESeq2 ExpressionData
updated 3.0 years ago by • 0 • written 3.0 years ago by ▴ 10
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2
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2.6k
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Using DESeq2 for Differential Expression Analysis with Interaction Term
DifferentialExpression GeneExpression DESeq2 Design()
3.4 years ago p.l.chen • 0
2
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2
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8.1k
views
Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 3.4 years ago by ★ 4.7k • written 3.4 years ago by ▴ 10
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2
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1.3k
views
Gene expression in R
limma edgeR Biobase GeneExpression
3.5 years ago sogol.bouyeh • 0
2
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2
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2.1k
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DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
3.7 years ago SUMIT • 0
5
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18
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3.6k
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DESeq2 comparison two cell types and two genotypes
GeneExpressionWorkflow DESeq2 GeneExpression
updated 3.8 years ago by 43k • written 3.9 years ago by • 0
1
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3
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1.2k
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DESeq analysis with Biological replicate.
DESeq2 ExpressionData GeneExpression
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
1
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1
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904
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Accounting for fish body mass in DE?
GeneExpression edgeR
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
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1
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935
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Find significant genes related to a specific disease
GeneExpression RNASeqR limma
updated 4.3 years ago by ▴ 510 • written 4.3 years ago by • 0
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3
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1.2k
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Troubles implementing LIMMA for paired samples (before/after treatment) comparaisons
GeneExpression R limma MultipleComparison
updated 4.3 years ago by 68k • written 4.3 years ago by • 0
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792
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Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
4.3 years ago coobzie • 0
2
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5
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13k
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Calculating FPKM from raw counts data using fpkm() in deseq2
deseq2 r fpkm() geneexpression
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 60
1
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4
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2.5k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 6.9 years ago by 21k • written 6.9 years ago by ▴ 10
3
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1
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2.1k
views
Processing several GSM from GEO database using Barcode and fRMA
frma barcode geneexpression gsm ncbi geo
updated 7.3 years ago by ▴ 830 • written 7.3 years ago by • 0
1
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4
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2.1k
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ddCT Package for StepOnePlus qPCR output
qPCR ddCt geneexpression
updated 7.6 years ago by ▴ 120 • written 7.6 years ago by ▴ 60
1
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3
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1.4k
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General suggestions regarding gene expression
geneexpression
updated 8.1 years ago by 52k • written 8.1 years ago by • 0
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0
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1.1k
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Where or how to find the gene interaction with itself?
microarray gene interaction geneexpression
8.2 years ago shaheryar • 0
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0
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1.3k
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Error in SAMseq analysis with R
r samseq microarray rnaseq geneexpression
8.5 years ago namilio • 0
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0
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1.4k
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Methylation and gene expression
methylation geneexpression
8.6 years ago Asma rabe ▴ 290
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2
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1.3k
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Methylation and gene expression data
methylation geneexpression
updated 8.8 years ago by ▴ 130 • written 8.8 years ago by ▴ 290
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3
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1.8k
views
error in drawing MDS plot for eset
MDSplot geneexpression insilicomerging
updated 9.0 years ago by 68k • written 9.0 years ago by ▴ 20
1
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6
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2.1k
views
how to deal the effect of enormous gene expression?
deseq2 rnaseq tomato geneexpression
updated 9.0 years ago by 43k • written 9.0 years ago by • 0
0
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1
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1.5k
views
Error in MetaQC R package.
r metaqc microarray geneexpression
9.2 years ago Agaz Hussain Wani ▴ 260
0
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3
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2.3k
views
problem with WGCNA
geneexpression
updated 9.3 years ago by ★ 3.0k • written 9.3 years ago by • 0
2
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5
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2.0k
views
heatmap in R
r language microarray geneexpression
updated 9.5 years ago by ★ 1.1k • written 9.5 years ago by • 0
1
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1
reply
1.4k
views
gene expression data analysis
microarray geneexpression
updated 9.5 years ago by 68k • written 9.5 years ago by • 0
1
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1
reply
5.5k
views
NA p and p adjusted value
geneexpression
updated 9.6 years ago by ★ 3.0k • written 9.6 years ago by • 0
1
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2
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6.6k
views
explanation of makeContrasts function of limma package
limma microarray R geneexpression
updated 9.6 years ago by ★ 28k • written 9.6 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: sesameDataCache is not work properly on my system by Samreen • 0
Any luck with this? I have tried all of the above and it still doesn't work. This is my session info and I'm on a cluster computing environ…
Answer: Using tximport for kallisto aligned TOIL data by James W. MacDonald 68k
If you just have the transcript data, you probably don't need (and maybe cannot use) `tximport`. Instead you could just do the naive thing …
Answer: Reading gene expression data in GPR format and converting it to xlsx format by James W. MacDonald 68k
Setting aside the inadvisability of putting these data into Excel (and I should point out that these data are not single-cell, but instead …
Comment: concentration tables suitable as input for new packages? by wilkinson • 0
I am grateful for your response. Software such as "Spectra" may parse MS-data to generate tables of concentrations, for instance. But inste…
Comment: Removing UTR from GTF for gene quantification by ATpoint ★ 4.7k
Consider asking at biostars or bioinformatics reddit, since this is not directly related to a Bioconductor problem. Anyway, a couple of th…
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Answer: Differential expression of proteins using somascan data
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Handle zero effective gene length when tximport RSEM results
Handle zero effective gene length when tximport RSEM results
How to remove genes with 0 counts in tximport?
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