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2
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1.3k
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summarizeToGene in tximeta causing vastly different results
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updated 2.7 years ago by 43k • written 2.7 years ago by • 0
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750
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updated 18 months ago by • 0 • written 2.7 years ago by • 0
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918
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Make custom Txdb class objects from Txdb
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2.7 years ago Shreyash ▴ 10
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fc value in ggmaplot does not correspond to the real lfc value on the plot
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updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
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12
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Unwanted variation observed on PCA for transcript level data
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updated 2.7 years ago by 43k • written 2.7 years ago by ▴ 10
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scRNAseq Download Errors
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updated 2.7 years ago by 4.2k • written 2.7 years ago by ★ 1.6k
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Speedglm dependency issue?
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2.7 years ago Kathleen Reed ▴ 20
0
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1
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1.0k
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Can't make a boxplot or hist with oligo
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updated 2.7 years ago by 68k • written 2.7 years ago by • 0
1
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2
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Error in getCdfInfo(object) :
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2.7 years ago kobra • 0
0
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0
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719
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Cannot generate plots when calling ChAMP
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2.7 years ago Kan • 0
0
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0
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Gene A mutation vs Gene B amplification using TCGA datasets
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2.7 years ago Begin-R • 0
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4
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How to get TPM / FPKM after batch correction with DESeq2?
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2.7 years ago vk • 0
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2.7 years ago Pilid • 0
0
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1
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773
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topGO: how do I retrieve my genes contributing to the GO term enrichment
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2.7 years ago Priya • 0
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16
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How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
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2.7 years ago Chris ▴ 20
2
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3
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Using gcrma() and using the t-test to compare single genes of interest for disease vs healthy comparison?
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updated 2.7 years ago by 68k • written 2.7 years ago by ▴ 10
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2
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1.3k
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error in champ.SVD
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updated 2.7 years ago by 4.2k • written 2.7 years ago by • 0
2
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2
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Error in checkFullRank(modelMatrix)
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updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 30
1
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2
replies
1.8k
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Filter by expression and keep probes in limma
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2.7 years ago Abdul ▴ 20
1
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1
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3.2k
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FPKM t-test vs DEseq2
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updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 10
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1
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EGSEA::egsea - Parallelization issue and "Error in array(col.rgb[, i], dim(node.rgb)[3:1]) : negative length vectors are not allowed"
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2.7 years ago neilzhao ▴ 30
0
votes
1
reply
872
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Can I use baseMean (from DESeq2) as part of presenting/ interpreting results
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updated 2.7 years ago by 43k • written 2.7 years ago by • 0
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4
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0
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2.7 years ago yuzun • 0
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2
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How to find the number of protein-coding genes in each chromosome arm in human?
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2.7 years ago Liliian • 0
0
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0
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Are LFQ workflow arguments from DEP package all required or optional?
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2.7 years ago aymanreffai • 0
2
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How to aggregate pseudobulks: Normalization & Log-Transformation
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2.7 years ago Tadeoye ▴ 20
1
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1
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858
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Performing a one-sided test for differential expression analysis in edgeR
edgeR
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
0
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Manually adjusting BCV for exactTest in edgeR based on plotBCV
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2.7 years ago f_rahmdani • 0
1
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1
reply
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Error with Pathview: Bad Request (HTTP 400)
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updated 2.7 years ago by ★ 4.1k • written 2.7 years ago by ▴ 10
4
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5
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EnhancedVolcano - Unable to customize the length of Connectors to Gene Labels
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4
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6
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DESeq2 for single cell pseudobulk processing
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0
votes
1
reply
573
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Package requires binary executable from external software?
external executable
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
0
votes
0
replies
829
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How to extract the counts for non-split reads from paired end RNA-seq data?
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2.7 years ago barrypraveen • 0
0
votes
1
reply
780
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Differential express genes in one group across all time points
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updated 2.7 years ago by 43k • written 2.7 years ago by • 0
4
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Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
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updated 18 months ago by • 0 • written 2.7 years ago by ▴ 10
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3
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1.7k
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Differential Expression Analysis between Clusters
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updated 2.7 years ago by • 0 • written 2.7 years ago by • 0
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5
replies
4.7k
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How to combine two DESeq2 objects (dds) for analysis
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updated 2.7 years ago by 43k • written 2.7 years ago by ▴ 10
1
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5
replies
2.9k
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How many parameters should be included in the model design for deseq2?
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2.7 years ago Weiqian ▴ 10
2
votes
2
replies
939
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How Can I Assess the Reliability of BCV (Square-Root Dispersion) in Non-Replicated Experiments for Differential Expression Analysis Using edgeR?
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2.7 years ago f_rahmdani • 0
1
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2
replies
1.5k
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Removing Unwanted Variations
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2.7 years ago AZ ▴ 30
1
vote
3
replies
1.3k
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Recount3 data correspond to TCGA data
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updated 10 months ago by ★ 1.1k • written 2.7 years ago by • 0
0
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1
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2.5k
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biomaRt - NameSpace loading failed
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updated 2.7 years ago by ★ 6.6k • written 2.7 years ago by • 0
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votes
2
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1.6k
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GSVA with and without absolute scaling method
GSVA
2.7 years ago arashdeep singh • 0
0
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1
reply
978
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Plotting read densities from DiffBind results
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updated 2.7 years ago by ★ 5.2k • written 2.7 years ago by ▴ 20
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votes
2
replies
1.2k
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Question regarding multiple comparisons in DiffBind
DiffBind
2.7 years ago epipally • 0
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Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reply Gordon. I am also working on the project and have been tasked to reformulate and add some details. We're interested i…
Answer: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…
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You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
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In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
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C: DESeq2 Following RSEM
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