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DESEQ2
•
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0
votes
1
reply
798
views
resultsNames(dds) is not similar to coldata(dds)?
DESeq2
3.5 years ago
A.J.
▴ 20
0
votes
2
replies
1.8k
views
How to get colData with GEOquery to prepare for DEseq2
GEOquery
DEseq2
3.5 years ago
Yugang
• 0
1
vote
1
reply
843
views
DESeq2 Multiple Pairwise Comparisons with Odd Set-up
MultipleComparison
DESeq2
updated 3.5 years ago by
Michael Love
43k • written 3.5 years ago by
Joshua
• 0
1
vote
2
replies
1.7k
views
How to properly use DESeq2 for an experiment
ExperimentalDesign
RNASeq
DifferentialExpression
DESeq2
updated 3.5 years ago by
Michael Love
43k • written 3.5 years ago by
Aurélien
• 0
0
votes
5
replies
4.6k
views
Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
DESE
DESeq2
updated 3.5 years ago by
Basti
▴ 780 • written 3.5 years ago by
Maryam.sed1400
• 0
0
votes
3
replies
3.3k
views
installation of package ‘DESeq2’ had non-zero exit status
DESeq2
updated 3.5 years ago by
ATpoint
★ 5.0k • written 3.5 years ago by
GA
▴ 10
0
votes
1
reply
1.7k
views
trouble installing DESeq2
install
packages
R
DESeq2
updated 3.5 years ago by
shepherl
4.2k • written 3.5 years ago by
eruan1
• 0
1
vote
5
replies
13k
views
is it possible to use TPM in DESeq2 ?
counts
Normalization
DESeq2
updated 3.5 years ago by
swbarnes2
★ 1.4k • written 3.5 years ago by
Hicham
▴ 10
0
votes
3
replies
3.2k
views
Cannot install DESeq2 to R 4.2 version
DESeq2
updated 3.5 years ago by
shepherl
4.2k • written 3.5 years ago by
Jae Woong
• 0
0
votes
1
reply
1.6k
views
BaseMean and Log2FC values seem weird...
DESeq2
updated 3.5 years ago by
ATpoint
★ 5.0k • written 3.5 years ago by
Anne
• 0
0
votes
2
replies
931
views
Volcano plots
DESeq2
written 3.5 years ago by
devi
• 0
1
vote
1
reply
954
views
ChIRP-seq peaks and GSEA
DESeq2
updated 3.5 years ago by
ATpoint
★ 5.0k • written 3.5 years ago by
Johnny
• 0
0
votes
1
reply
2.7k
views
DESeq2- how to remove NA values
DESeq2
updated 3.5 years ago by
Kevin Blighe
★ 4.0k • written 3.5 years ago by
devi
• 0
2
votes
3
replies
1.9k
views
Problem with tximport IDs
tximport
tx2gene
rnas
DESeq2
RNASeqData
3.6 years ago
Maka
• 0
1
vote
2
replies
1.4k
views
Technical replicates of different library from same sample
DESeq2
3.6 years ago • updated 3.5 years ago
myfam128
• 0
5
votes
14
replies
7.4k
views
Possible ways to select differential expressed genes using DeSeq2 or edgeR
R
deseq2
edger
differential gene expression
fold change
updated 3.6 years ago by
ATpoint
★ 5.0k • written 7.4 years ago by
Beginner
▴ 60
0
votes
8
replies
3.5k
views
Error in SummarizedExperiment
DESeq2
3.6 years ago
Talpham
• 0
0
votes
1
reply
3.9k
views
DESeq2 installation Error (ERROR: dependency ‘locfit’ is not available for package ‘DESeq2’)
DESeq2
updated 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
tsomakiank
• 0
4
votes
5
replies
3.4k
views
DESeq2::plotPCA plotting error
RStudio
PCA
DESeq2
written 3.6 years ago by
960942
• 0
0
votes
1
reply
577
views
Deseq2 high outlier number
DESeq2
updated 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
Davide
• 0
1
vote
8
replies
6.1k
views
deseq2 normalized counts as an input to deseq2
DESeq2
updated 2.6 years ago by
Michael Love
43k • written 3.6 years ago by
Elif
• 0
1
vote
6
replies
6.9k
views
BaseMean threshold
basemean
DESeq2
updated 3.2 years ago by
ATpoint
★ 5.0k • written 3.6 years ago by
msellabenton
• 0
0
votes
3
replies
894
views
Student
samples
sampleNumbers
DESeq2
written 3.6 years ago by
Lidia
• 0
10
votes
6
replies
16k
views
DESEq2 VST error
deseq2
variancestabilizingtransformation
updated 3.3 years ago by
Muhammad
• 0 • written 8.3 years ago by
anpham
▴ 70
0
votes
4
replies
1.5k
views
Extremely different results for both EdgeR and DESeq2 analysis
edgeR
DESeq2
updated 3.6 years ago by
Gordon Smyth
53k • written 3.6 years ago by
melatoninixo
• 0
1
vote
3
replies
1.4k
views
Why are padj results different for BetaPrior = TRUE vs lfcShrink()?
IHW
lfcShrink
DESeq2
3.6 years ago
Ali Barry
▴ 40
1
vote
5
replies
2.1k
views
Potential outlier/high variance
deseq
DESeq2
updated 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
Amali Thrimawithana
• 0
0
votes
2
replies
2.5k
views
Error in DESeq(dds) : is(object, "DESeqDataSet") is not TRUE
DESeq2
3.6 years ago
ng.akingbesote
• 0
16
votes
12
replies
3.9k
views
VST transformation (DESeq2) for metabolomics data
vst
Metabolomics
DESeq2
3.6 years ago
Joan Miró
▴ 80
2
votes
1
reply
2.8k
views
Deseq2 for 16s Data
Microbiome
16s
Deseq2
16srRNA
updated 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
Katelyn
▴ 10
1
vote
2
replies
3.0k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq
DifferentialExpression
DESeq2
3.6 years ago
Ismail
• 0
1
vote
7
replies
12k
views
Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no pa…
DESeq2
updated 3.5 years ago by
Michael Love
43k • written 3.6 years ago by
cbravo11
• 0
0
votes
5
replies
3.3k
views
Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData
isoform
DESeq2
3.6 years ago • updated 3.5 years ago
priyanka.m
• 0
1
vote
2
replies
1.1k
views
how to change the FDR threshold in DESrq2?
DESeq2
3.6 years ago • updated 3.5 years ago
devi
• 0
10
votes
11
replies
4.0k
views
Counts from recount3 for DESeq2 analysis
recount3
DESeq2
updated 3.2 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.6 years ago by
william.benit
▴ 10
0
votes
3
replies
1.7k
views
lfcShrink contrast
lfcshrink
R
DESeq2
updated 3.6 years ago by
ATpoint
★ 5.0k • written 3.6 years ago by
LHA_trash
• 0
0
votes
1
reply
1.2k
views
DESeq2 with small sample size
DESeq2
updated 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
jjeang
• 0
3
votes
6
replies
2.6k
views
Paired sample design in DESeq2
DESeq2
updated 3.6 years ago by
Jae Hyung Jung
▴ 10 • written 4.0 years ago by
Liam
• 0
0
votes
1
reply
863
views
batch effects for a single sample?
DESeq2
updated 3.6 years ago by
swbarnes2
★ 1.4k • written 3.6 years ago by
nute11a
▴ 10
2
votes
1
reply
1.3k
views
DESeq2
DESeq2
updated 3.6 years ago by
Basti
▴ 780 • written 3.6 years ago by
edusbioinfo
• 0
0
votes
2
replies
4.1k
views
Incorporating spike-ins to rna-seq analysis
Spike-in
RNASeqR
DESeq2
Normalization
rna-seq
updated 2.2 years ago by
manuel.fernandez
• 0 • written 3.6 years ago by
cicely.day
• 0
0
votes
2
replies
1.6k
views
Condition shown as 'Untreated vs. Treated' in output of results() in DESeq2
RNASeqData
DESeq2
updated 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
treebig44
▴ 40
0
votes
1
reply
1.1k
views
Getting erros from dds
DifferentialExpression
DESeq2
updated 3.6 years ago by
swbarnes2
★ 1.4k • written 3.6 years ago by
beslinail
• 0
0
votes
3
replies
1.2k
views
DESeq2 relevel question and resultsNames
DESeq2
updated 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
Hannah
• 0
0
votes
4
replies
1.2k
views
DESeq2 Volcano - Quick Question
DESeq2
3.6 years ago
axe880
• 0
0
votes
7
replies
2.1k
views
DESeq2 on allelic reads
RNASeq
DifferentialExpression
DESeq2
updated 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
Nayrouz
• 0
0
votes
1
reply
1.3k
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics
DESeq2
metagenomeSeq
edgeR
KEGG
updated 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
Aditya
• 0
3
votes
2
replies
1.9k
views
filterbyexprs before DESeq2
DESeq2
3.6 years ago
luca.s
▴ 50
0
votes
1
reply
905
views
How to add new column name to empty header in a list elements
DESeq2
updated 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
kcm
• 0
2
votes
4
replies
1.4k
views
how to save results meta data to file
DESeq2
written 3.8 years ago by
aedavids
▴ 20
4,838 results • Page
22 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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