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Showing :
DESEQ2
•
reset
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
yuet
• 0
2
votes
2
replies
2.8k
views
Time series and interaction in DESeq2
DESeq2
3.6 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 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
dadca596
• 0
0
votes
2
replies
2.0k
views
DESeq2 comparisons with multiple experimental variables?
DESeq2
updated 3.6 years ago by
swbarnes2
★ 1.4k • written 3.6 years ago by
Roland
• 0
0
votes
1
reply
966
views
DeSeq2 timecourse analysis
RNAseqRData
DeSeq2
updated 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
Hannah
• 0
1
vote
2
replies
1.3k
views
Setting up read count data for DESeq2 to create a dds object
DESeq2
updated 3.6 years ago by
swbarnes2
★ 1.4k • written 3.6 years ago by
Adam
• 0
1
vote
1
reply
975
views
mgcv not loading on an update
m1_arm
deseq2
updated 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
Modoc Kesner
▴ 10
0
votes
1
reply
791
views
DESeq how to evaluate design fit
DESeq2
updated 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
aedavids
▴ 20
1
vote
4
replies
1.6k
views
lncRNA Differential Expression Analysis
DESeq2
limma
RNASeqData
3.6 years ago
sushimoto
• 0
0
votes
1
reply
975
views
DEG for multiple comparisons
DESeq2
3.6 years ago
rand.alkaissy
• 0
0
votes
2
replies
1.3k
views
Subsetting DESEQ2 VST Microbiome Data
DESeq2
16S
VST
3.6 years ago
vollkorrn
• 0
0
votes
5
replies
2.7k
views
DESeqDataSetFromMatrix Function Error
DESeq2
Bioconductor
updated 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
Kevin
• 0
0
votes
3
replies
1.3k
views
DEseq2 Analysis over multiple tissues and conditions only gives 16 coefficients
DESeq2
RNASeq
updated 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
niko.fleischer
• 0
0
votes
2
replies
2.9k
views
DESeq2 counts distribution across both genes and samples
deseq2
rnaseq
updated 3.6 years ago by
BarryGutierrez
• 0 • written 9.2 years ago by
igor
▴ 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
Michael Love
43k • written 3.7 years ago by
vanbelj
▴ 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
sunnet.ys
• 0 • written 5.1 years ago by
takisliako
• 0
2
votes
2
replies
895
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
Gordon Smyth
53k • written 3.7 years ago by
Raito92
▴ 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
Michael Love
43k • written 3.7 years ago by
JaneDoe
• 0
1
vote
8
replies
3.0k
views
lfcShrink MA plot comparison
DESeq2
updated 3.7 years ago by
Michael Love
43k • written 3.7 years ago by
user230613
• 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
Michael Love
43k • written 3.7 years ago by
dario.beraldi
• 0
0
votes
6
replies
1.7k
views
ScRNA sequencing data _Seurat_Object_DESEQ2_Analayis_DGE
DESeq2
updated 3.7 years ago by
Michael Love
43k • written 3.7 years ago by
Jehan
• 0
6
votes
2
replies
972
views
The number of controls versus treatment in differential expression analysis
DESeq2
edgeR
limma
updated 3.7 years ago by
Gordon Smyth
53k • written 3.7 years ago by
AZ
▴ 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
Michael Love
43k • written 3.7 years ago by
treebig44
▴ 40
2
votes
4
replies
5.5k
views
Making contrasts for multiple treatment groups using DESeq2
DESeq2
updated 3.2 years ago by
Michael Love
43k • written 3.7 years ago by
Manav
• 0
4
votes
4
replies
1.3k
views
Covariates to be included in DE model
DESeq2
limma
updated 2.8 years ago by
Michael Love
43k • written 3.7 years ago by
forlani.luca
• 0
0
votes
3
replies
1.6k
views
dealing with outliers (deseq2)
maxcooks
outliers
zero
counts
DESeq2
updated 3.7 years ago by
Michael Love
43k • written 3.7 years ago by
andreia
▴ 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
972
views
Including covariates from bulkRNAseq deconvolution to look for differentially expressed genes
DESeq2
updated 3.7 years ago by
Michael Love
43k • written 3.7 years ago by
ross.smith
• 0
1
vote
1
reply
1.0k
views
Strange error while running DESeq() function.
DESeq2
RNASeq
RNASeqData
updated 3.7 years ago by
Michael Love
43k • written 3.7 years ago by
treebig44
▴ 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
1.8k
views
Identifying DEG between development stages
plant
Transcriptomics
DESeq2
r
updated 3.7 years ago by
Basti
▴ 780 • written 3.7 years ago by
cicely.day
• 0
1
vote
4
replies
2.6k
views
Unable to run "library(DESeq2)" successfully
DESeq2
written 4.8 years ago by
Hui
• 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
Michael Love
43k • written 3.7 years ago by
mat.lesche
▴ 110
2
votes
2
replies
1.2k
views
Could use some advice on analyzing ranks of expressed genes in two conditions,
GeneExpression
DESeq2
ExpressionData
updated 3.7 years ago by
fivescarynightsgames
• 0 • written 3.7 years ago by
reza
▴ 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
3.7 years ago
jordi.planells
• 0
0
votes
1
reply
844
views
Some warnings when downloading "DESeq2"
DESeq2
updated 3.7 years ago by
Michael Love
43k • written 3.7 years ago by
Ziyi Qi
• 0
3
votes
3
replies
2.4k
views
Deseq2 normalization steps
deseq2
normalization
updated 3.7 years ago by
Michael Love
43k • written 6.5 years ago by
santamariagianluca
• 0
1
vote
3
replies
1.3k
views
scale of mu in assays(dds)
DESeq2
3.7 years ago
chase.mateusiak
• 0
2
votes
5
replies
2.0k
views
DESeq2 with baseline correction for gene expression differences
DESeq2
edgeR
Transcriptomics
updated 3.7 years ago by
Michael Love
43k • written 3.7 years ago by
R1337
• 0
2
votes
5
replies
4.1k
views
DESeq2 and high prefiltering cutoff
DESeq2
prefiltering
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
Michael Love
43k • written 3.7 years ago by
vanbelj
▴ 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
3.7 years ago • updated 3.6 years ago
9906201a
▴ 20
1
vote
1
reply
979
views
Result table pvalue and adjusted p value
DESeq2
updated 3.7 years ago by
Michael Love
43k • written 3.7 years ago by
Bine
▴ 50
0
votes
2
replies
947
views
Differential expression in fixed windows
DESeq2
RNASeq
3.7 years ago
anatmela
• 0
1
vote
2
replies
12k
views
Error in SummarizedExperiment(assays = SimpleList(counts = countData)
DESeq2
3.7 years ago
Hanan
• 0
2
votes
1
reply
1.2k
views
DESeq2 handling of replicates
DESeq2
RNASeq
limma
updated 3.7 years ago by
Michael Love
43k • written 3.7 years ago by
Eyal
• 0
4
votes
3
replies
1.9k
views
Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2
idep
RNASeqData
updated 3.7 years ago by
swbarnes2
★ 1.4k • written 3.7 years ago by
student2
▴ 10
0
votes
5
replies
7.3k
views
DESeq2/Differential expression analysis without replicates
DESeq2
DEG
updated 3.2 years ago by
bioinfomagics
• 0 • written 3.8 years ago by
priya.dalvi
• 0
4,838 results • Page
23 of 97
Recent ...
Replies
Answer: mzR-Rcpp compiler version issue
by
Laurent Gatto
1.6k
There are two issues here. First, a warning about mzR, that you can safely ignore. It tells you that mzR was compiled using a different …
Comment: Identifying differentially expressed genes in individual samples from a large co
by
jamie.gearing
▴ 60
Great. Yes, something descriptive is probably good enough, even if the p-values themselves are not so rigorous. Thanks very much Gordon!
Comment: Co-occurrence Network Analysis between Algae and Bacteria
by
Stefano Mangiola
▴ 40
Just a placeholder, that we are extending `sccomp` to co-occurrence analyses. Yours could be a good use-case to test first. We will be in t…
Answer: DESeq2 design for haplotype MPRA
by
aimesd808
• 0
I appreciate you telling me about this. Now it's crystal plain to me. Publish this: https://support.bioconductor.org/p/9162649/
Answer: Extract snp information from genomic regions with biomaRt -> "oaries_snp"
by
Kevin Blighe
★ 4.0k
My sincere apologies that my colleagues had ignored your question. The error occurs because the "chromosomal_region" filter is not valid…
Votes
Answer: Identifying differentially expressed genes in individual samples from a large co
Answer: Identifying differentially expressed genes in individual samples from a large co
Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Comment: Error installing Seqinfo
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