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1
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464
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putting my own expression data in deseq2
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updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
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updated 19 months ago by 68k • written 19 months ago by • 0
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Could we detect difference at pathway level but not significant different at gene level?
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Dominance Index for Shotgun Metagenomics Data
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updated 19 months ago by ▴ 40 • written 19 months ago by ★ 1.6k
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PCA plot suggestions
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updated 19 months ago by 43k • written 19 months ago by • 0
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Deseq2. decontXcounts not integers. Useful alternative?
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updated 19 months ago by 43k • written 19 months ago by • 0
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ATACseq merge peaks
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updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
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Improving the design matrices vignette in RNAseq123
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19 months ago Lluís Revilla Sancho ▴ 760
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Math expression in shapeCustom legend in EnhancedVolcano
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19 months ago pl23 • 0
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9
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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updated 19 months ago by 68k • written 19 months ago by • 0
0
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One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
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19 months ago glaciya2018 • 0
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19 months ago ATpoint ★ 5.0k
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
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updated 19 months ago by 43k • written 19 months ago by • 0
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how to do Differential splicing from SGSeq analysis
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19 months ago Sara • 0
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get BM error
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How to retrieve gene ontology GO class from gene list?
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Exon-exon Junction Analysis for Variable-length Exons
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Opposite sign of LFC in count plots of DEGs (DESeq2)
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19 months ago winwater0928 • 0
3
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
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updated 19 months ago by 43k • written 19 months ago by ▴ 40
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Citation for edgeR user guide
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755
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Cannabis OrgDb
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updated 19 months ago by ★ 1.4k • written 19 months ago by • 0
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19 months ago info ▴ 10
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minfi::read.metharray.exp
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featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
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19 months ago shuwangxinze1996 • 0
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written 19 months ago by • 0
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updated 19 months ago by 68k • written 19 months ago by • 0
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FDR via q-value
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updated 14 months ago by 68k • written 19 months ago by • 0
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19 months ago catv • 0
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19 months ago fernanda.backsouza ▴ 30
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Why p value inconsistent when using different number of pathway score?
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19 months ago Chris ▴ 20
0
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0
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I am trying to detect alternative splicing.
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19 months ago Sebashish • 0
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Error retrieving ensembl gene id using biomaRt...
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Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
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19 months ago BioinfGuru ▴ 70
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FilterByExpr low counts with small sample size
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19 months ago Jonathan ▴ 10
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19 months ago prity6459 • 0
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3
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updated 19 months ago by 53k • written 19 months ago by • 0
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updated 19 months ago by 53k • written 19 months ago by • 0
0
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FGSEA pre-ranked input in increasing order or decreasing
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updated 18 months ago by ▴ 280 • written 19 months ago by • 0
0
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 19 months ago by ★ 1.9k • written 19 months ago by • 0
46,691 results • Page 25 of 934
Recent ...
Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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