Showing : DeSeq2 • reset
2
votes
2
replies
1.2k
views
[DESeq2] There is no difference in expression in my heatmap
DESeq2 heatmaps
2.9 years ago Sooni ▴ 10
0
votes
1
reply
926
views
Extracting interaction contrast when using user supplied model.matrix
DESeq2
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
1
vote
3
replies
1.4k
views
DESeq2 Installation Issue
DESeq2
updated 2.9 years ago by 16k • written 2.9 years ago by • 0
2
votes
4
replies
1.4k
views
Calculated contrasts in DESeq2: difference between manual coefficients and DESeq2 authomatic contrast
DESeq2 DifferentialExpression
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
1
reply
841
views
Rnaseq analysis using a continuous time series
DESeq2
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
2
replies
1.7k
views
installing DESeq2 on Macbook R Studio
DESeq2
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
1
reply
471
views
More information on results columns
DESeq2
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
0
votes
1
reply
879
views
How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2 RNASeqData DifferentialExpression
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
1
vote
3
replies
3.7k
views
Do the count values should be only integer to be able to use DESeq2?
DESeq2
2.9 years ago Sep • 0
0
votes
5
replies
1.6k
views
Error running DESeq2 on longitudinal data: Error in checkFullRank(modelMatrix)
DESeq2 longitudinal
updated 2.9 years ago by ★ 1.4k • written 2.9 years ago by ▴ 40
0
votes
1
reply
1.2k
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 2.9 years ago by ★ 1.6k • written 2.9 years ago by ▴ 10
4
votes
7
replies
1.7k
views
DESeq2: Repetitive padj values?
DESeq2
updated 2.9 years ago by 43k • written 2.9 years ago by ▴ 30
1
vote
1
reply
1.0k
views
Is this DESeq2 interactions design correct?
DESeq2 interactions
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
3
replies
1.4k
views
how to iterate all comparisons in group with "coef =" ?
DESeq2
updated 2.9 years ago by 43k • written 2.9 years ago by ▴ 10
0
votes
1
reply
2.9k
views
Variance stabilization transformation (VST), blind=TRUE
DESeq2 Transcriptomics RNASeq
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
1
reply
1.1k
views
Help for RNA sequencing analysis with DESEQ2
DESeq2 star differentiallyexpressed
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
1
vote
3
replies
1.5k
views
Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2 edgeR rnaseqGene
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
1
reply
741
views
Combining VST counts for replicates
DESeq2
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
1
reply
1.6k
views
How to set threshold of padj value in DeSeq2
DESeq2 padj default
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
0
votes
1
reply
766
views
Differential RNA seq on TCGA set
DESeq2 RNASeqData
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
0
votes
1
reply
473
views
rlog() transformation works only when using DESeqDataSet, not matrix
DESeq2
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
2
replies
770
views
Differential expression between samples of the same group
DESeq2
2.9 years ago Oded • 0
0
votes
1
reply
1.5k
views
Missing transcript
DESeq2 tximport salmon
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
1
vote
3
replies
1.7k
views
Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2 TCGAbiolinks
2.9 years ago Alexandre • 0
1
vote
4
replies
2.5k
views
Inverted Log2FC values after DEseq2 analysis
DESeq2 Log2FC RNASeqData
2.9 years ago Iwan • 0
0
votes
3
replies
1.3k
views
Differential gene expression analysis with data matrix generated with RSEM
DESeq2 edgeR
2.9 years ago ubjw24 • 0
1
vote
1
reply
1.1k
views
Using the standard deviation of DESeq rlog transformed counts to identify genes for hierarchical clustering
DESeq2
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
1
vote
3
replies
9.3k
views
Manually calculating log2 fold change values from DESeq2 normalized counts
DESeq2 DifferentialExpression
2.9 years ago Jayesh Kumar • 0
0
votes
3
replies
1.4k
views
Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
4
replies
1.4k
views
suggest to report differential count estimate in DESeq2
DESeq2
2.9 years ago Yongqing • 0
2
votes
5
replies
2.7k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 21 months ago by 43k • written 2.9 years ago by • 0
1
vote
6
replies
1.7k
views
low counts from microRNA seq
DESeq2 microRNA HTSeq
2.9 years ago abhay.kanodia • 0
0
votes
2
replies
1.5k
views
DESeq2: overlap differentially expressed genes with and without interaction term
DESeq2
2.9 years ago xuscha • 0
1
vote
3
replies
4.1k
views
Error in SummarizedExperiment in DESeq2
DESeq2
3.0 years ago Cherif • 0
0
votes
3
replies
1.6k
views
DESeq2 Statistic - Padj NA
DESeq2 RNAseq123 rnaseq deseq2 metatranscriptomic
updated 2.9 years ago by 43k • written 3.0 years ago by • 0
0
votes
1
reply
1.4k
views
DeSeq2 and GenomicRange installation possible conflict with bioconductor version 3.16?
DESeq2 version3.16 installation bioconductor GenomicRange
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
1
vote
2
replies
2.2k
views
running DESeq2 from nanopore wf-alignment workflow
DESeq2 NanoporeRNASeq
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
votes
2
replies
1.4k
views
Analyzing barcode sequencing experiments with DESeq2/edgeR
edgeR DESeq2
updated 3.0 years ago by • 0 • written 3.4 years ago by • 0
0
votes
2
replies
1.3k
views
TnSeq as ZINB? Alternatives in R?
DESeq2 R edgeR Python TnSeq
updated 3.0 years ago by • 0 • written 3.0 years ago by ▴ 90
0
votes
3
replies
2.3k
views
Unusual MA and volcano plots?
DESeq2 RNASeq
written 3.0 years ago by ▴ 10
0
votes
1
reply
676
views
How does DESeq2 handle multiple conditions in one design.
DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
votes
1
reply
1.1k
views
Correction for multiple comparison by DeSeq2 - treatment1 vs. control, treatment2 vs. control, ... treatment n vs. control
DESeq2 MultipleComparison r
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
votes
1
reply
912
views
Using DESeq2 for time-series analysis with two conditions
DESeq2 RNASeqData
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
0
votes
1
reply
1.2k
views
Log2FC in LRT vs Wald in multifactorial design
DESeq2 LRT multifactorial up/down-reg log2FC
updated 3.0 years ago by 68k • written 3.0 years ago by ▴ 10
0
votes
2
replies
1.3k
views
Results analysis of differential gene expression using DESeq2 package
RnaSeqSampleSize statistics DESeq2
updated 3.0 years ago by ★ 1.4k • written 3.0 years ago by • 0
0
votes
2
replies
1.3k
views
How to filter for counts in different columns
DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
votes
3
replies
1.5k
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
votes
2
replies
862
views
checkFullRank(modelMatrix) while neither factor can be predicted from each other.
DESeq2
updated 3.0 years ago by ★ 1.4k • written 3.0 years ago by ▴ 10
1
vote
13
replies
3.0k
views
Deseq2 , result() taking too long > 3hrs
DESeq2
updated 2.8 years ago by • 0 • written 3.0 years ago by • 0
4
votes
8
replies
3.5k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 2.5 years ago by 53k • written 3.0 years ago by ▴ 20
4,840 results • Page 16 of 97
Recent ...
Replies
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 …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Votes
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
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.2k
Popular Question to Gordon Smyth 53k
Locations • All
The city by the bay, 11 minutes ago
China, 15 minutes ago
United States, 45 minutes ago
United States, 45 minutes ago
United States, 1 hour ago
Traffic: 586 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6