Showing : DeSeq2 • reset
0
votes
1
reply
915
views
How to add new column name to empty header in a list elements
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
2
votes
4
replies
1.4k
views
how to save results meta data to file
DESeq2
written 3.8 years ago by ▴ 20
2
votes
17
replies
3.3k
views
How to reduce the impact of one varaible in Deseq2 or edgeR for multivariate value analysis?
MultipleComparison edgeR DESeq2
written 3.7 years ago by • 0
2
votes
2
replies
2.8k
views
Time series and interaction in DESeq2
DESeq2
3.7 years ago Francesco ▴ 10
0
votes
2
replies
2.4k
views
DESeq2 Log2 fold change does not make sense given change in TPM
DESeq2 TPM Foldchange
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
0
votes
2
replies
2.0k
views
DESeq2 comparisons with multiple experimental variables?
DESeq2
updated 3.7 years ago by ★ 1.4k • written 3.7 years ago by • 0
0
votes
1
reply
970
views
DeSeq2 timecourse analysis
RNAseqRData DeSeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
1
vote
2
replies
1.3k
views
Setting up read count data for DESeq2 to create a dds object
DESeq2
updated 3.7 years ago by ★ 1.4k • written 3.7 years ago by • 0
1
vote
1
reply
984
views
mgcv not loading on an update
m1_arm deseq2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 10
0
votes
1
reply
795
views
DESeq how to evaluate design fit
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 20
1
vote
4
replies
1.6k
views
lncRNA Differential Expression Analysis
DESeq2 limma RNASeqData
3.7 years ago sushimoto • 0
0
votes
1
reply
983
views
DEG for multiple comparisons
DESeq2
3.7 years ago rand.alkaissy • 0
0
votes
2
replies
1.3k
views
Subsetting DESEQ2 VST Microbiome Data
DESeq2 16S VST
3.7 years ago vollkorrn • 0
0
votes
5
replies
2.7k
views
DESeqDataSetFromMatrix Function Error
DESeq2 Bioconductor
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
0
votes
3
replies
1.3k
views
DEseq2 Analysis over multiple tissues and conditions only gives 16 coefficients
DESeq2 RNASeq
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
0
votes
2
replies
2.9k
views
DESeq2 counts distribution across both genes and samples
deseq2 rnaseq
updated 3.7 years ago by • 0 • written 9.3 years ago by ▴ 50
1
vote
1
reply
1.1k
views
DESeq2 With Ratios from Nascent RNA-seq (Conversion Rate from slamdunk)
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 30
0
votes
5
replies
17k
views
Error:The design matrix has the same number of samples and coefficients to fit, so estimation of dispersion is not possible. Treating samples as …
deseq2
updated 3.7 years ago by • 0 • written 5.2 years ago by • 0
2
votes
2
replies
903
views
Salmon counts for a gene but it is not in my DESeq2 tables
DESeq2
3.7 years ago tomtom ▴ 10
15
votes
18
replies
5.1k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2 edgeR goana GO
updated 3.7 years ago by 53k • written 3.7 years ago by ▴ 60
0
votes
1
reply
1.1k
views
LRT test in DESeq2 decide on the level of comparisons
DESeq2 LRT Model
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
1
vote
8
replies
3.0k
views
lfcShrink MA plot comparison
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
3
votes
4
replies
2.5k
views
Large difference between naive log2 and rlog transformation of count data
DESeq2 Normalization rlog
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
0
votes
6
replies
1.7k
views
ScRNA sequencing data _Seurat_Object_DESEQ2_Analayis_DGE
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
6
votes
2
replies
982
views
The number of controls versus treatment in differential expression analysis
DESeq2 edgeR limma
updated 3.7 years ago by 53k • written 3.7 years ago by ▴ 30
4
votes
1
reply
3.7k
views
Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2 RNASeq RNASeqData
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 40
2
votes
4
replies
5.5k
views
Making contrasts for multiple treatment groups using DESeq2
DESeq2
updated 3.2 years ago by 43k • written 3.7 years ago by • 0
4
votes
4
replies
1.3k
views
Covariates to be included in DE model
DESeq2 limma
updated 2.8 years ago by 43k • written 3.7 years ago by • 0
0
votes
3
replies
1.6k
views
dealing with outliers (deseq2)
maxcooks outliers zero counts DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 10
2
votes
2
replies
1.2k
views
Confounding DE results with DESeq2
isoforms DESeq2
3.7 years ago arfranco ▴ 130
0
votes
1
reply
978
views
Including covariates from bulkRNAseq deconvolution to look for differentially expressed genes
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
1
vote
1
reply
1.0k
views
Strange error while running DESeq() function.
DESeq2 RNASeq RNASeqData
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 40
4
votes
6
replies
13k
views
How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2 RNASeq RNASeqData
3.7 years ago treebig44 ▴ 40
1
vote
3
replies
1.9k
views
Identifying DEG between development stages
plant Transcriptomics DESeq2 r
updated 3.7 years ago by ▴ 780 • written 3.7 years ago by • 0
1
vote
4
replies
2.6k
views
Unable to run "library(DESeq2)" successfully
DESeq2
written 4.8 years ago by • 0
0
votes
1
reply
1.1k
views
DESeq2 TimeCourse with alpha and ihw and genes that change up to a certain timepoint
TimeCourse DESeq2 Manual
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 110
2
votes
2
replies
1.3k
views
Could use some advice on analyzing ranks of expressed genes in two conditions,
GeneExpression DESeq2 ExpressionData
updated 3.7 years ago by • 0 • written 3.7 years ago by ▴ 10
1
vote
4
replies
1.4k
views
Using DESeq2 to analyze m6A read counts from Nanopore sequencing
DESeq2
3.7 years ago YC • 0
0
votes
4
replies
1.6k
views
DESeq2 pseudotime series design?
DESeq2 design
3.8 years ago • updated 3.7 years ago jordi.planells • 0
0
votes
1
reply
848
views
Some warnings when downloading "DESeq2"
DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
3
votes
3
replies
2.4k
views
Deseq2 normalization steps
deseq2 normalization
updated 3.8 years ago by 43k • written 6.5 years ago by • 0
1
vote
3
replies
1.3k
views
scale of mu in assays(dds)
DESeq2
3.8 years ago chase.mateusiak • 0
2
votes
5
replies
2.0k
views
DESeq2 with baseline correction for gene expression differences
DESeq2 edgeR Transcriptomics
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
2
votes
5
replies
4.1k
views
DESeq2 and high prefiltering cutoff
DESeq2 prefiltering
3.8 years ago • updated 3.7 years ago Chris • 0
4
votes
7
replies
2.2k
views
DESeq2: Subset Results from 2-Factor Design
DESeq2
updated 3.7 years ago by 43k • written 3.8 years ago by ▴ 30
5
votes
5
replies
3.1k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
3.8 years ago • updated 3.6 years ago 9906201a ▴ 20
1
vote
1
reply
986
views
Result table pvalue and adjusted p value
DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 50
0
votes
2
replies
966
views
Differential expression in fixed windows
DESeq2 RNASeq
3.8 years ago anatmela • 0
1
vote
2
replies
12k
views
Error in SummarizedExperiment(assays = SimpleList(counts = countData)
DESeq2
3.8 years ago Hanan • 0
2
votes
1
reply
1.2k
views
DESeq2 handling of replicates
DESeq2 RNASeq limma
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
4,840 results • Page 23 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
Commentator to sina.nassiri ▴ 130
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
Locations • All
Pittsburgh, United States, 1 minute ago
United States, 33 minutes ago
Switzerland/Lausanne, 1 hour ago
Germany, 1 hour ago
United Kingdom, 1 hour ago
Traffic: 953 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