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Deseq2
•
reset
0
votes
3
replies
2.2k
views
DESeq2 package unrecognized after downloading latest version of R: keep getting erros
DESeq2
updated 2.4 years ago by
ATpoint
★ 5.0k • written 2.4 years ago by
saguiar
• 0
0
votes
1
reply
833
views
Design formula for genotype-specific condition effects using ~group in the design
RNASeqData
DifferentialExpression
DESeq2
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
james.zhang20
• 0
0
votes
5
replies
1.3k
views
Wondering how to look at the reads of a gene in samples to check if it was knocked out?
knockout
DESeq2
written 2.4 years ago by
Lillian
• 0
0
votes
4
replies
1.5k
views
DESEq2 Error: rows did not converge
DESeq2
2.4 years ago
andrebolerbarros
▴ 20
0
votes
2
replies
1.1k
views
Can DESeq2 handle low number of samples and replicates?
DESeq2
updated 2.4 years ago by
ATpoint
★ 5.0k • written 2.4 years ago by
Rockbar
• 0
2
votes
5
replies
2.3k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 19 months ago by
Ashley
• 0 • written 2.4 years ago by
zxc741xb
• 0
1
vote
4
replies
1.6k
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue
Spati
RSEM
deno
DEseq2
written 2.5 years ago by
shashank
• 0
1
vote
3
replies
1.2k
views
DESeq: relaxing gene filtering thresholds increases mean-Sd correlation, but recovers many important genes
metaanalysis
meanSd
genefilter
DESeq2
2.4 years ago
Ndimensional
▴ 20
2
votes
8
replies
1.9k
views
Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge
beta
DESeq2
2.4 years ago
Ndimensional
▴ 20
0
votes
5
replies
1.4k
views
Model and Contrasts with 4 variables
contrast
edgeR
DESeq2
updated 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
Cristina
• 0
0
votes
1
reply
513
views
Is there a way to solve "the model matrix is not full rank", when just one of my sample is showing batch effect?
DESeq2
updated 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
Jung E. Ji
• 0
0
votes
17
replies
4.9k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2
differential expression
error
updated 2.4 years ago by
snow34
• 0 • written 8.1 years ago by
ap3637
• 0
0
votes
1
reply
723
views
DESeq2 how to extract expression values corresponding to log2FoldChange
DESeq2
updated 2.4 years ago by
ATpoint
★ 5.0k • written 2.4 years ago by
Raissa
• 0
0
votes
1
reply
800
views
Comparing DGE between datasets with uneven sample sizes using DESeq2
unevensamplesizes
ComparingDGEresults
DESeq2
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
reba.duncan
• 0
1
vote
1
reply
711
views
Deseq contrast question
RNASeqData
DESeq2
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
Hannah
▴ 10
0
votes
4
replies
1.2k
views
Using different filtering steps in different iterations of DEseq2
DESeq2
2.4 years ago
marinaw
▴ 20
1
vote
2
replies
923
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts
DESeq2
2.4 years ago
jovel_juan
▴ 30
0
votes
2
replies
1.1k
views
Can DESeq2 handle huge variations in sequencing depth among samples?
HugevariationsinsequencingDepth
DESeq2
2.4 years ago
Gopinath
• 0
0
votes
4
replies
2.0k
views
Discrepancy between DESeq2 files produced in Galaxy and R(RStudio)
DESeq2
updated 21 months ago by
kethselly
• 0 • written 2.4 years ago by
peTTU
• 0
0
votes
1
reply
609
views
Several questions about the workflow using DESeq2 to process RNA data
DESeq2
updated 2.4 years ago by
ATpoint
★ 5.0k • written 2.4 years ago by
liuyang32201220
▴ 20
1
vote
3
replies
4.9k
views
DeSEQ 2 Error: some values in assay are negative
Countmatrix
negativeassay
DESeq2
2.4 years ago
dania.khalid
• 0
2
votes
2
replies
1.4k
views
DESeq2 on multilevel design variable
DESeq2
updated 2.4 years ago by
swbarnes2
★ 1.4k • written 2.4 years ago by
Amdom
• 0
0
votes
1
reply
1.1k
views
DESeq2 + analysis question for design with uneven time point design
timecourse
KEGG
DESeq2
updated 2.4 years ago by
Michael Love
43k • written 2.5 years ago by
Fred
• 0
0
votes
2
replies
2.3k
views
Handling NA's in Deseq2
Dese
DESeq2
2.4 years ago
Asger Mølgaard
• 0
0
votes
2
replies
1.3k
views
Remove duplicate genera in DEseq output?
DESeq2
updated 2.4 years ago by
Lluís Revilla Sancho
▴ 760 • written 2.4 years ago by
Bretta
• 0
0
votes
2
replies
1.5k
views
Can VST-transformed community composition data be expressed as relative abundance?
vst
relativeabundance
Normalization
DESeq2
2.5 years ago • updated 2.4 years ago
dwas
• 0
3
votes
6
replies
1.6k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 2.5 years ago by
Gordon Smyth
53k • written 2.5 years ago by
mohammedtoufiq91
▴ 10
1
vote
2
replies
1.0k
views
Normalized counts from LRT or Wald test?
DESeq2
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
sneha108ss
• 0
2
votes
1
reply
879
views
DESeq2 or edgeR for Presence and Absence of Proteins
edgeR
DESeq2
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
calvincornell1996
• 0
0
votes
2
replies
1.3k
views
DoparParam() execution fails when foreach() works
clustermq
doparallel
DESeq2
2.5 years ago
boris
• 0
0
votes
2
replies
1.8k
views
Nanostring data differential expression analysis: limma or DESeq2?
DESeq2
NanoStringDiff
limma
2.5 years ago
pg45863
▴ 10
0
votes
1
reply
1.0k
views
how to solve this error
DESeq2
GEO
miRNAData
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
ashisaanz
• 0
0
votes
4
replies
1.4k
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor
Transcriptomics
DifferentialExpression
DESeq2
2.5 years ago
sreeshmaraj72
• 0
0
votes
1
reply
967
views
DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2
RNASeqData
edgeR
limma
DifferentialExpression
updated 2.5 years ago by
swbarnes2
★ 1.4k • written 2.5 years ago by
simon
• 0
2
votes
9
replies
7.0k
views
how to control age and gender effect in expression data using DESeq2
deseq2
rnaseq
mirna-seq
differential gene expression
written 7.7 years ago by
klalit1803
▴ 10
3
votes
3
replies
1.9k
views
Subsetting DESeq data set to compare treatments within one group (multi-group experiment)
DifferentialExpression
DESeq2
updated 2.5 years ago by
swbarnes2
★ 1.4k • written 2.5 years ago by
tinattn.nguyen
▴ 20
1
vote
2
replies
1.8k
views
Batch effect between biological replicates
BatchEffect
DESeq2
2.5 years ago
gtechbio
▴ 10
1
vote
3
replies
1.1k
views
Find if one gene has a significantly different Log2FC than a different gene
DESeq2
updated 2.5 years ago by
Michael Love
43k • written 2.5 years ago by
Matt
• 0
0
votes
3
replies
1.3k
views
Dispersion outliers genes
Dispersion
DESeq2
2.5 years ago
raya.fai
▴ 60
0
votes
1
reply
1.2k
views
Which file in tximport should I use for DESeq2 analysis?
tximport
DESeq2
updated 2.5 years ago by
James W. MacDonald
68k • written 2.5 years ago by
Yijing
• 0
0
votes
2
replies
1.9k
views
about baseMean in DEseq2
DESeq2
written 4.3 years ago by
Bogdan
▴ 670
3
votes
3
replies
1.4k
views
Rlog performed on tpm or raw transcript abundances?
DESeq2
rlog
written 2.9 years ago by
Bioinformatics-414
• 0
0
votes
2
replies
1.1k
views
Accounting for technical replicates in DESeq2
DESeq2
updated 2.5 years ago by
swbarnes2
★ 1.4k • written 2.5 years ago by
sara.p
• 0
3
votes
1
reply
1.0k
views
Applying DESeq2 to (suspected) Poisson distributed gene expression data (in the case of pseudoreplication)
DESeq2
updated 2.5 years ago by
Michael Love
43k • written 2.5 years ago by
Thomas
• 0
2
votes
1
reply
1.4k
views
scaledTPM for DESeq2 using tximport
DESeq2
tximport
updated 2.5 years ago by
Michael Love
43k • written 2.5 years ago by
prangannathofficial
• 0
2
votes
7
replies
3.0k
views
optimHess problem in apeglm/DESeq2
DESeq2
apeglm
updated 2.5 years ago by
Michael Love
43k • written 2.5 years ago by
ATpoint
★ 5.0k
1
vote
2
replies
1.1k
views
Obtention of the binomial transformed count table with edgeR
DESeq2
edgeR
RNASeq
DifferentialExpression
updated 2.5 years ago by
Gordon Smyth
53k • written 2.5 years ago by
Sofía
• 0
0
votes
1
reply
799
views
DESeq2: Comparison between 1 test sample with 1 control sample
DESeq2
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
Vivek
• 0
2
votes
17
replies
3.4k
views
lfcshrink error DESeq2
DESeq2
lfcshrink
DESe
updated 2.5 years ago by
Michael Love
43k • written 2.5 years ago by
Alina
• 0
0
votes
2
replies
842
views
Deseq2 design
DESeq2
genes
Differential
expressed
2.5 years ago
Syed Zaheer
▴ 10
4,836 results • Page
12 of 97
Recent ...
Replies
Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
by
Matthew Thornton
▴ 380
WOW! Thank you so much for the information. I will do this.
Comment: "Watched Tags" are being erased rather than updated
by
RalphSavage99
• 0
Thanks for sharing https://github.com/Bioconductor/support.bioconductor.org/issues/112
Answer: Add additional maintainer for MOFA2
by
shepherl
4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
Answer: After running samtools, the featureCounts command crashed.
by
Kevin Blighe
★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot
by
Kevin Blighe
★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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