Showing : DESEQ2 • reset
1
vote
3
replies
1.3k
views
RSEM and Tximport
RSEM tximport deseq2
updated 5.4 years ago by 68k • written 5.4 years ago by • 0
1
vote
3
replies
1.5k
views
interaction models DESeq2
deseq2 interaction model
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 90
0
votes
1
reply
576
views
RNA Targeted Ampliseq Data analysis - What approach to prefer?
ampliseq rna targeted edger deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 60
0
votes
1
reply
872
views
Error while importing RSEM counts using DESeqDataSetFromTximport function
deseq2
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
2
votes
4
replies
819
views
size factor not 1
deseq2
updated 5.5 years ago by ★ 1.4k • written 5.5 years ago by ▴ 40
1
vote
3
replies
2.0k
views
deseq2 - paired samples in 2 sequencing types with very different library sizes
deseq2
updated 4.6 years ago by 43k • written 5.5 years ago by • 0
0
votes
2
replies
6.7k
views
plotPCA with DESeq2 results in unable to find an inherited method for function plotPCA for signature matrix Error
deseq2 pheatmap RColorBrewer BiocGenerics
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
3
votes
4
replies
3.0k
views
Reporting S values? Reporting padj values?
deseq2 apeglm
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 20
0
votes
1
reply
1.6k
views
DESeq2: error message
deseq2
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by • 0
0
votes
5
replies
1.3k
views
DEseq2 2x2 design using a grouping variable
deseq2 ~group
5.5 years ago weichengz ▴ 10
1
vote
7
replies
1.2k
views
Extracting results for a single chromosome
deseq2
5.5 years ago Charlotte • 0
0
votes
2
replies
660
views
How to perform contrasts within groups
deseq2
5.5 years ago Charlotte • 0
1
vote
4
replies
5.4k
views
Non-integer values in salmon counts change DE analyses
deseq2
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by • 0
0
votes
3
replies
593
views
Determining sample size in contrast groups
deseq2
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by • 0
2
votes
1
reply
1.8k
views
Cross-species analysis and normalization with DESeq2
normalization deseq2 across species rnaseq
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
votes
6
replies
2.0k
views
DESeq2 log2foldchange shows opposite sign than clearly visible in pseudocounts or vst values (correct order in contrast)
deseq2 log2FoldChange
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
1
vote
3
replies
875
views
Differential gene expression analysis
deseq2
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 10
0
votes
7
replies
2.8k
views
DESeq error: Error in validityMethod(object) : nrow(design) == ncol(object) is not TRUE
deseq2 DESeq nrow == ncol is not TRUE
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by • 0
1
vote
6
replies
1.4k
views
Rescaling predictors in DESeq changes outcomes?
deseq2 glm rescale
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 10
0
votes
3
replies
1.7k
views
DESeq2: Subset dataset or use interaction in design
deseq2
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
votes
3
replies
2.1k
views
Strange p values for DEG analysis with covariates using DESeq2
deseq2 edgeR salmon tximport
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
votes
6
replies
793
views
How to treat genes in RNAseq analyses
deseq2
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
0
votes
1
reply
991
views
DESeq2 Experiment Setup
deseq2 Tutorial
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
votes
1
reply
2.2k
views
Installing DESeq2 on R 3.6.2 fails, due to package "foreign" being unavailable
deseq2
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
2
votes
1
reply
691
views
small number of significant gene
deseq2
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by ▴ 40
0
votes
2
replies
3.5k
views
Normalisation of rlog and VSD transformation
deseq2 rna-seq R
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by ▴ 10
1
vote
9
replies
1.5k
views
Use of coef() as a measure of effect size in a multiple regression using DESeq2
DESeq2 GLMs
updated 4.2 years ago by ▴ 10 • written 5.5 years ago by • 0
0
votes
4
replies
994
views
Some confuse in ?results example of DESeq2
deseq2
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 40
3
votes
8
replies
4.6k
views
Normalisation in DESeq2
deseq2 rna-seq
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by ▴ 10
1
vote
3
replies
7.7k
views
DeSeq2 error: counts matrix should be numeric, currently it has mode: character
deseq2
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
1
vote
3
replies
2.6k
views
Pairwise comparison of multiple groups with different base
deseq2 rna-seq r
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 10
1
vote
8
replies
2.9k
views
[Outlier Gene removal] - One sample with outlier counts for some genes
RNAseq DESeq2 outlier counts DE analysis
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by • 0
0
votes
2
replies
762
views
Conducting differential variability analysis with DESeq2
deseq2 variation
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
votes
1
reply
8.1k
views
How to make PCA plot using DESeq2 for a group design
deseq2
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by ▴ 10
4
votes
10
replies
4.2k
views
how to analyze WGCNA results?
cancer probe deseq2 annotation normalization
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by ▴ 10
2
votes
3
replies
2.1k
views
DESeq2 LRT test for multi-factor designs
deseq2
updated 3.7 years ago by 43k • written 5.5 years ago by • 0
0
votes
1
reply
900
views
DESeq2 for normalizing metagenomic counts
deseq2
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
votes
2
replies
602
views
How to find differential gene and expression analysis using DESeq or edgeR
edger deseq2
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
1
vote
1
reply
777
views
Meeting Questions when using Deseq2paper package
deseq2
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by • 0
2
votes
7
replies
1.1k
views
lfcShrink giving error
deseq2
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by ▴ 10
4
votes
7
replies
5.9k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by • 0
0
votes
8
replies
1.6k
views
To start organising data for DESeq2
deseq2
updated 5.5 years ago by ★ 1.4k • written 5.5 years ago by ▴ 10
0
votes
2
replies
1.1k
views
Extraction of individual results from DESeq2 data
deseq2
updated 5.5 years ago by ★ 1.4k • written 5.5 years ago by • 0
1
vote
1
reply
748
views
correct use of regularized log/VST values from deseq2
deseq2
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
1
vote
7
replies
3.8k
views
High padj in DESeq2
deseq2 RNA-seq microRNA
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by ▴ 10
4
votes
5
replies
1.9k
views
DESeq2 Error from Installing a Package
deseq2
updated 5.5 years ago by 25k • written 5.5 years ago by ▴ 10
0
votes
1
reply
716
views
pacbio long reads into DESeq2
deseq2
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
2
votes
2
replies
2.8k
views
How to Analyse Datasets from GEO
geo rnaseq deseq2 tpm
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by ▴ 10
2
votes
3
replies
741
views
DESEQ2 error after adding batch in design
deseq2
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by • 0
2
votes
1
reply
1.9k
views
DESeq Data Set From Matrix
deseq2
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 40
4,839 results • Page 39 of 97
Recent ...
Replies
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much, @ATpoint and @kevin , for your valuable insights. I have carefully checked all your suggestions. First, I examined th…
Answer: Finding duplicated entries in GRangesList by Kevin Blighe ★ 4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: DESeq2 on non-RNASeq counts data by Kevin Blighe ★ 4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hello Rui Tang, The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
The issue that you describe with the tumor mutational burden (TMB) plots appearing linear and lacking consistent TMB values across samples …
Votes
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
Awards • All
Scholar to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Supporter to fabio.marroni • 0
Popular Question to Guido Hooiveld ★ 4.1k
Popular Question to James W. MacDonald 68k
Locations • All
United States, 20 minutes ago
Germany, 34 minutes ago
United States, 35 minutes ago
United States, 1 hour ago
Pittsburgh, United States, 1 hour ago
Traffic: 492 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