Showing : GeneExpression • reset
2
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"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression Clustering ctsGE
9 weeks ago jbgnielson • 0
2
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2
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409
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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
5 months ago Manthos • 0
2
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3
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1.6k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 7 months ago by 50k • written 7 months ago by • 0
0
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1
reply
478
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Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
9 months ago Arianna • 0
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2
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1.8k
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FeatureCounts Output Counts at Exon Level Using Default Settings, want gene level
GeneExpression
12 months ago CDSPARKS ▴ 10
0
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1
reply
632
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Heatmap of two conditions from the normalized gene count data
GeneExpression heatmaps
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
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1
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2.4k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
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4
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1.7k
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Comparing different method for DESEQ2
DESeq2 GeneExpression
updated 19 months ago by 41k • written 19 months ago by • 0
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3
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1.0k
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CountOverlap
GeneExpression ChIPSeqData
updated 19 months ago by 65k • written 19 months ago by ▴ 20
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1
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1.9k
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GDCprepare of STAR - counts
GeneExpression TCGAbiolinks
updated 19 months ago by • 0 • written 2.0 years ago by • 0
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0
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443
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Free Gibbson energy RNA doublex
GeneExpression RNAinteract
20 months ago Tamina • 0
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0
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575
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Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
22 months ago hlee ▴ 10
0
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2
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932
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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 22 months ago by ★ 1.3k • written 22 months ago by • 0
0
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1
reply
538
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Error "DESeqDataSetFromMatrix" function not found
GeneExpression
updated 22 months ago by ▴ 780 • written 22 months ago by • 0
0
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1
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634
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Aggregate differentially expressed genes across all contrast results using DEVis
DifferentialExpression NanoporeRNASeq DESeq2 GeneExpression DEVis
updated 23 months ago by 65k • written 23 months ago by • 0
1
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1
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771
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Error while using champ.SVD function
GeneExpression
updated 2.0 years ago by ▴ 780 • written 2.0 years ago by • 0
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0
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850
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Volcano plot: Putting calculated values in legend
GeneExpression
updated 2.1 years ago by ★ 3.9k • written 2.1 years ago by • 0
2
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2
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822
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Could use some advice on analyzing ranks of expressed genes in two conditions,
GeneExpression DESeq2 ExpressionData
updated 2.1 years ago by • 0 • written 2.2 years ago by ▴ 10
0
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2
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2.0k
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Using DESeq2 for Differential Expression Analysis with Interaction Term
DifferentialExpression GeneExpression DESeq2 Design()
2.6 years ago p.l.chen • 0
2
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2
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6.8k
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Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 2.6 years ago by ★ 4.1k • written 2.6 years ago by ▴ 10
0
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2
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962
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Gene expression in R
limma edgeR Biobase GeneExpression
2.7 years ago sogol.bouyeh • 0
2
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2
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1.6k
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DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
2.9 years ago SUMIT • 0
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18
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2.9k
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DESeq2 comparison two cell types and two genotypes
GeneExpressionWorkflow DESeq2 GeneExpression
updated 3.0 years ago by 41k • written 3.0 years ago by • 0
1
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3
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969
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DESeq analysis with Biological replicate.
DESeq2 ExpressionData GeneExpression
updated 3.3 years ago by 41k • written 3.3 years ago by • 0
1
vote
1
reply
733
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Accounting for fish body mass in DE?
GeneExpression edgeR
updated 3.3 years ago by 65k • written 3.3 years ago by • 0
0
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1
reply
751
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Find significant genes related to a specific disease
GeneExpression RNASeqR limma
updated 3.4 years ago by ▴ 510 • written 3.4 years ago by • 0
1
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3
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967
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Troubles implementing LIMMA for paired samples (before/after treatment) comparaisons
GeneExpression R limma MultipleComparison
updated 3.4 years ago by 65k • written 3.4 years ago by • 0
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0
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621
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Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
3.5 years ago coobzie • 0
2
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5
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11k
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Calculating FPKM from raw counts data using fpkm() in deseq2
deseq2 r fpkm() geneexpression
updated 5.6 years ago by 41k • written 5.6 years ago by ▴ 60
1
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4
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2.0k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 6.1 years ago by 21k • written 6.1 years ago by ▴ 10
3
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1
reply
1.7k
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Processing several GSM from GEO database using Barcode and fRMA
frma barcode geneexpression gsm ncbi geo
updated 6.5 years ago by ▴ 830 • written 6.5 years ago by • 0
1
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4
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1.8k
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ddCT Package for StepOnePlus qPCR output
qPCR ddCt geneexpression
updated 6.8 years ago by ▴ 120 • written 6.8 years ago by ▴ 60
1
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3
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1.2k
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General suggestions regarding gene expression
geneexpression
updated 7.2 years ago by 50k • written 7.2 years ago by • 0
0
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0
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906
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Where or how to find the gene interaction with itself?
microarray gene interaction geneexpression
7.4 years ago shaheryar • 0
0
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0
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1.2k
views
Error in SAMseq analysis with R
r samseq microarray rnaseq geneexpression
7.7 years ago namilio • 0
0
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0
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1.2k
views
Methylation and gene expression
methylation geneexpression
7.7 years ago Asma rabe ▴ 290
0
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2
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1.1k
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Methylation and gene expression data
methylation geneexpression
updated 8.0 years ago by ▴ 130 • written 8.0 years ago by ▴ 290
0
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3
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1.6k
views
error in drawing MDS plot for eset
MDSplot geneexpression insilicomerging
updated 8.1 years ago by 65k • written 8.1 years ago by ▴ 20
1
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6
replies
1.8k
views
how to deal the effect of enormous gene expression?
deseq2 rnaseq tomato geneexpression
updated 8.2 years ago by 41k • written 8.2 years ago by • 0
0
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1
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1.3k
views
Error in MetaQC R package.
r metaqc microarray geneexpression
8.4 years ago Agaz Hussain Wani ▴ 260
0
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3
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1.8k
views
problem with WGCNA
geneexpression
updated 8.5 years ago by ★ 3.0k • written 8.5 years ago by • 0
2
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5
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1.7k
views
heatmap in R
r language microarray geneexpression
updated 8.7 years ago by ★ 1.0k • written 8.7 years ago by • 0
1
vote
1
reply
1.2k
views
gene expression data analysis
microarray geneexpression
updated 8.7 years ago by 65k • written 8.7 years ago by • 0
1
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1
reply
5.1k
views
NA p and p adjusted value
geneexpression
updated 8.7 years ago by ★ 3.0k • written 8.7 years ago by • 0
1
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2
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5.7k
views
explanation of makeContrasts function of limma package
limma microarray R geneexpression
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 10
0
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3
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11k
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How to combine expression values of multiple probes for one gene
probe convert geneexpression onechannelgui
updated 8.8 years ago by ▴ 830 • written 8.8 years ago by ▴ 10
0
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0
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1.1k
views
Using segAnglePo() for a set of genes
geneexpression genesetenrichment segAnglePo
9.4 years ago Peter.Wood • 0
3
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5
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8.5k
views
limma voom accessing normalised counts tables
limma rnaseq geneexpression voom counts
updated 9.5 years ago by ★ 13k • written 9.5 years ago by ▴ 10
9
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7
replies
9.3k
views
DESeq2 timecourse - How to set the experimental design
deseq2 geneexpression timecourse
updated 9.6 years ago by ★ 13k • written 9.6 years ago by ▴ 10
4
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2
replies
4.0k
views
Selecting genes based on expressional variance
geneexpression wgcna rnaseq
updated 9.6 years ago by 1.6k • written 9.6 years ago by ▴ 250
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Comment: Help with running egsea() by James W. MacDonald 65k
I don't understand the last question, but do look at the msigdb.gsets argument to `buildIdx` in the help page for that function.
Votes
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
Answer: How to save the DEXSeq results
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