Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
deseq2
•
reset
0
votes
2
replies
463
views
DESeq2 sizefactors counfounded with biological treatment
DESeq2
11 months ago • updated 10 months ago
Anna
• 0
1
vote
2
replies
780
views
Deseq2 res Function
DESeq2
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
sap275
▴ 10
0
votes
4
replies
711
views
Help with RSEM counts: do I transpose matrix?
RSEM
DESeq2
11 months ago
NB
• 0
0
votes
5
replies
750
views
Identical samples after deseq2 batch effect removal
DESeq2
updated 11 months ago by
Michael Love
43k • written 11 months ago by
maripane
• 0
0
votes
1
reply
554
views
DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
Raya
• 0
1
vote
2
replies
474
views
Differene between the Wald and LRT test for time-series gene expression data
DESeq2
11 months ago
Denise
• 0
0
votes
1
reply
396
views
eRNAs count
RNASeq
DESeq2
updated 11 months ago by
ATpoint
★ 5.0k • written 11 months ago by
Irene
• 0
0
votes
1
reply
596
views
DESeq2 rerun returns different results
DESeq2
updated 11 months ago by
ATpoint
★ 5.0k • written 11 months ago by
wl1111
• 0
0
votes
1
reply
502
views
Is my time course analysis with DESeq2 valid?
GeneExpression
DESeq2
TimeCourse
updated 11 months ago by
Michael Love
43k • written 11 months ago by
Jason
• 0
0
votes
1
reply
536
views
DESeq2 "Not full rank" and "less than full rank" error
DESeq2
deseq
updated 11 months ago by
Guido Hooiveld
★ 4.1k • written 11 months ago by
Najla Abassi
• 0
2
votes
2
replies
1.0k
views
Handling biological replicates in DESeq2
DESeq2
updated 11 months ago by
ATpoint
★ 5.0k • written 11 months ago by
sk
• 0
5
votes
3
replies
29k
views
DESeq2: thousands of NA for pvalues?
deseq2
rna-seq
DEGs
cooks cutoff
written 6.8 years ago by
aishu.jp
▴ 30
1
vote
6
replies
1.5k
views
Volcano plot has many values around zero
RNA-seq
DESeq2
volcanoplot
updated 11 months ago by
Michael Love
43k • written 11 months ago by
nramakr
▴ 10
0
votes
2
replies
564
views
DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 11 months ago by
ballackselma
• 0
4
votes
5
replies
1.3k
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
11 months ago
LuciaNhu
• 0
0
votes
1
reply
716
views
Average expression of genes across replicates
DESeq2
updated 11 months ago by
ATpoint
★ 5.0k • written 11 months ago by
James
• 0
0
votes
0
replies
390
views
News:
RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2
GenomicRanges
11 months ago
info
▴ 10
0
votes
11
replies
2.4k
views
Question about using LRT test for time course experiments with DESeq2
DESeq2
updated 6 months ago by
Rob
• 0 • written 11 months ago by
Denise
• 0
0
votes
1
reply
552
views
Deseq to output continous sequencing data
DESeq2
updated 11 months ago by
Michael Love
43k • written 12 months ago by
Neha
• 0
1
vote
4
replies
1.3k
views
Adjusted p-values become NA when sub-setting samples
DESeq2
12 months ago • updated 11 months ago
txema.heredia
• 0
3
votes
3
replies
1.5k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma
edgeR
DESeq2
MAST
written 12 months ago by
Satoshi
• 0
0
votes
2
replies
738
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2
ESTIMATE
RNASeqData
MCPcounter
written 12 months ago by
Aleksandra
• 0
0
votes
1
reply
484
views
Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 12 months ago by
Michael Love
43k • written 12 months ago by
nicolettacommins
• 0
2
votes
3
replies
1.3k
views
Analysis of large RNA-Seq Datasets
DESeq2
updated 12 months ago by
Michael Love
43k • written 12 months ago by
KokiBio
• 0
1
vote
4
replies
1.1k
views
DESeq2 - interactions when using factors concatenated into group
DESeq2
12 months ago
boczniak767
▴ 740
0
votes
1
reply
357
views
2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
12 months ago
JY
• 0
0
votes
1
reply
442
views
How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 12 months ago by
Michael Love
43k • written 12 months ago by
agamemnon
• 0
0
votes
2
replies
470
views
how to extract expression matrix post deseq2
DESeq2
written 12 months ago by
agamemnon
• 0
0
votes
2
replies
506
views
Using Normalized Counts in DESeq2
DESeq2
updated 12 months ago by
Michael Love
43k • written 12 months ago by
KokiBio
• 0
3
votes
2
replies
566
views
When running contrasts, does it use normalized read counts?
DESeq2
12 months ago
Katherine
▴ 20
0
votes
1
reply
402
views
How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 12 months ago by
swbarnes2
★ 1.4k • written 12 months ago by
Bingqian
• 0
3
votes
4
replies
1.2k
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization
DESeq2
rlog
vst
12 months ago
Eva
▴ 10
1
vote
4
replies
1.2k
views
Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq
DESeq2
Oddresults
updated 12 months ago by
ATpoint
★ 5.0k • written 12 months ago by
Ricardo Iván
• 0
0
votes
1
reply
497
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression
ImpulseDE2
DESeq2
updated 12 months ago by
Michael Love
43k • written 12 months ago by
Jiahao Tian
• 0
2
votes
4
replies
843
views
RNASeq Time Course Question
DESeq2
RNASeq
TimeCourse
12 months ago
jihoon.kim.1495
▴ 10
0
votes
6
replies
1.3k
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression
DESeq2
BatchEffect
updated 12 months ago by
Michael Love
43k • written 12 months ago by
CriticalPeriod
• 0
5
votes
4
replies
962
views
How to control batch effect if Group and batch are same?
limma
DESeq2
BatchEffect
updated 12 months ago by
ATpoint
★ 5.0k • written 12 months ago by
Bioinformagician
• 0
0
votes
2
replies
629
views
RNA-Seq p value range variation
DESeq2
pvalue
RNA-Seq
12 months ago
paul.meraner
• 0
0
votes
0
replies
550
views
News:
RNAseq data analysis with Bioconductor (online course)
DESeq2
SummarizedExperiment
12 months ago • updated 11 months ago
info
▴ 10
1
vote
6
replies
1.4k
views
heatmap with batch effect
DESeq2
BatchEffect
written 12 months ago by
tothuhien
• 0
0
votes
2
replies
693
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport
DESeq2
updated 12 months ago by
Michael Love
43k • written 12 months ago by
oguzhankaraosmanoglu
• 0
1
vote
1
reply
964
views
Deseq2 sfType
Microbiome
DESeq2
RNASeq
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
Caroline
• 0
1
vote
1
reply
550
views
Normalization RNA-seq for multiple plates
Normalization
DESeq2
RNASeqData
edgeR
updated 12 months ago by
ATpoint
★ 5.0k • written 12 months ago by
Pimpa
• 0
1
vote
1
reply
572
views
DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 12 months ago by
ATpoint
★ 5.0k • written 12 months ago by
picasa1983
• 0
1
vote
2
replies
846
views
Poor dispersion fit in DESeq2
limma
DESeq2
RNASeq
edgeR
updated 13 months ago by
Michael Love
43k • written 13 months ago by
Ben
▴ 10
0
votes
2
replies
983
views
DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
DESeq2
updated 13 months ago by
Michael Love
43k • written 13 months ago by
duplessisantzel
• 0
1
vote
2
replies
1.0k
views
DESeq2 design and contrasts with 2 drug-treated and one control group
DESeq2
Bioconductor
updated 13 months ago by
Michael Love
43k • written 13 months ago by
JT
▴ 10
1
vote
6
replies
1.7k
views
New to Deseq2 - DEG questions / MA plot
genomes
DESeq2
Transcriptomics
updated 12 months ago by
ATpoint
★ 5.0k • written 13 months ago by
Newbie
• 0
0
votes
1
reply
452
views
Many DEGs (Is a high percentage of DEGs acceptable in DESeq2)?
DESeq2
updated 13 months ago by
Michael Love
43k • written 13 months ago by
madivinakristidiscar
• 0
17
votes
9
replies
8.2k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 13 months ago by
James W. MacDonald
68k • written 9.4 years ago by
ompandey
▴ 10
4,835 results • Page
3 of 97
Recent ...
Replies
Comment: DESeq2 for candidate gene analysis
by
piffelpaff
▴ 10
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis
by
Michael Love
43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Comment: Join BOC Sciences at Drug Discovery Chemistry
by
teamardigen
• 0
Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
Votes
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Join BOC Sciences at Drug Discovery Chemistry
Drug datasets for RNA-seq
Comment: Check removeBatchEffect effectiveness
Awards
• All
Popular Question
to
Hervé Pagès
16k
Popular Question
to
jf1
• 0
Popular Question
to
Gordon Smyth
53k
Popular Question
to
dan.gatti
• 0
Popular Question
to
shepherl
4.2k
Locations
• All
The city by the bay,
5 minutes ago
San Diego,
30 minutes ago
United States,
1 hour ago
United Kingdom,
1 hour ago
United States,
1 hour ago
Traffic: 795 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