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0
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0
replies
4
views
DESeq2 on non-RNASeq counts data
DESeq2
1 hour ago
vs
• 0
0
votes
0
replies
16
views
sigDF object in sesame
sesame
sesameData
3 hours ago
Ramiro
• 0
0
votes
0
replies
181
views
News:
Bioconductor Board Nominations Open
TAB
Bioconductor
CAB
4 weeks ago • updated 11 hours ago
shepherl
4.2k
3
votes
4
replies
7.8k
views
Calculation of module membership in WGCNA
WGCNA
RNA-seq
ModuleMembership
Network
Hub gene
written 5.0 years ago by
Arindam
▴ 80
0
votes
5
replies
141
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2
scRNAseq
updated 4 hours ago by
ATpoint
★ 4.9k • written 2 days ago by
Raya
• 0
0
votes
10
replies
204
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse
DESeq2
updated 9 hours ago by
James W. MacDonald
68k • written 4 days ago by
Denise
• 0
3
votes
3
replies
149
views
p-adjusted values in multiple comparisons
StatisticalMethod
limma
RnaSeqSampleSizeData
updated 3 days ago by
Gordon Smyth
52k • written 4 days ago by
ocanorocabayera
• 0
1
vote
5
replies
167
views
Are voomByGroup and voomLmFit compatible?
limma
voomLmFit
voomByGroup
updated 1 day ago by
Gordon Smyth
52k • written 5 days ago by
richardallenfriedmanbrooklyn
▴ 30
2
votes
6
replies
267
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
6 days ago • updated 5 days ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
3
replies
97
views
DESeq2 inconsistent fits depending on model design with interacting factors
des
DESeq2
written 6 days ago by
fedor.bezrukov
▴ 10
0
votes
2
replies
97
views
Create consensusMatrix for codon bases
Biostrings
updated 7 days ago by
James W. MacDonald
68k • written 7 days ago by
Hassan
• 0
1
vote
1
reply
86
views
Can limma be used with module eigengenes instead of genes?
limma
WGCNA
GSVA
updated 8 days ago by
Gordon Smyth
52k • written 8 days ago by
A.Barden
▴ 10
0
votes
2
replies
494
views
Job:
Job: Ensembl Genebuild Project Leader
JobPosting
ensembldb
written 10 weeks ago by
Aleena_Ensembl
▴ 30
1
vote
2
replies
124
views
The default value of 'abundanceCol'
tximportData
11 days ago • updated 8 days ago
Jinghua
• 0
1
vote
2
replies
139
views
Testing KO vs WT at day4/day14 with interactions in edgeR
scRNAseq
updated 9 days ago by
Gordon Smyth
52k • written 10 days ago by
Noah
• 0
2
votes
9
replies
400
views
Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq
edgeR
LongRead
Transcript
10 days ago • updated 8 days ago
mohammedtoufiq91
▴ 10
1
vote
2
replies
157
views
Difference between logFC in limma-voom and weighted limma-voom
limma
voom
weighting
12 days ago • updated 10 days ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
11
replies
642
views
emptyDrops new default alpha = Inf giving far fewer non-empty droplets than under old default of alpha = NULL
scrn
10x
scRNAseq
emptyDrops
DropletUtils
14 days ago • updated 5 days ago
Peter Hickey
▴ 760
0
votes
0
replies
44
views
Memory error while running alignments
DECIPHER
Alignment
14 days ago
Mihir
• 0
0
votes
0
replies
5
views
Spam:
Chat GPT Gratuit
chipenrich
procoil
14 days ago
Lệ
0
2
votes
1
reply
152
views
Limpa Pipeline Order
limma
limpa
updated 14 days ago by
Gordon Smyth
52k • written 14 days ago by
abadgerw
• 0
2
votes
2
replies
219
views
Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
limma
updated 13 days ago by
Gordon Smyth
52k • written 16 days ago by
A.Barden
▴ 10
3
votes
12
replies
334
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave
DESeq2
updated 1 day ago by
Michael Love
43k • written 20 days ago by
Aurélie
• 0
0
votes
8
replies
365
views
How to use limma to analyze complex temporal RNAseq data
timecourse
RNASeq
limma
16 days ago • updated 12 days ago
Jiahao Tian
• 0
3
votes
7
replies
447
views
makeChipPackage(): Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows:
AnnotationForge
updated 7 days ago by
James W. MacDonald
68k • written 19 days ago by
Jaqueline
• 0
2
votes
2
replies
197
views
Limma : paired samples leading to unexpected estimates
limma
21 days ago • updated 20 days ago
Basti
▴ 780
2
votes
2
replies
234
views
(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
21 days ago
sandmann.t
▴ 70
0
votes
1
reply
93
views
muffz.plot2
Mfuzz
updated 22 days ago by
James W. MacDonald
68k • written 22 days ago by
xiao
• 0
0
votes
2
replies
157
views
BiocManager::install() doesn't work
Install
Biocond
updated 21 days ago by
Marcel Ramos
700 • written 22 days ago by
flying_breadman
• 0
0
votes
4
replies
697
views
Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm
s-value
DESeq2
updated 16 days ago by
Michael Love
43k • written 4 weeks ago by
Erika
• 0
0
votes
1
reply
159
views
Feedback needed on new user-friendly BED file tool
bedbaser
offtopic
updated 22 days ago by
James W. MacDonald
68k • written 23 days ago by
nadia
• 0
1
vote
2
replies
269
views
Differential expression on the transcript-level
DESeq2
updated 23 days ago by
swbarnes2
★ 1.4k • written 25 days ago by
泓朴
• 0
0
votes
0
replies
73
views
CRISPRSeek Question: changing weight and gRNA.size causes error
CRISPRseek
CRISPR
updated 27 days ago by
James W. MacDonald
68k • written 27 days ago by
Citrus
• 0
0
votes
0
replies
61
views
Empty boxes in treemap plot rrvgo package
rrvgo
27 days ago
Asma
• 0
0
votes
3
replies
290
views
DEP R-package run_app ("TMT") spits this error: "Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'".
DEP
27 days ago • updated 13 days ago
Shajahan
• 0
3
votes
11
replies
1.7k
views
Highly DE genes but small count difference within conditions
RNASeq
DESeq2
RNASeqData
written 10 months ago by
bioshot.com
• 0
3
votes
2
replies
699
views
Transcript expression analysis using EdgeR
edgeR
Transcript
RNASeq
28 days ago • updated 27 days ago
mohammedtoufiq91
▴ 10
0
votes
0
replies
84
views
Results with PON give more variants
mutect2
variants
pon
29 days ago
ramiro.barrantes
▴ 10
0
votes
1
reply
152
views
ORFik: spliced 5utr regions
splicing
5utr
ORFik
updated 28 days ago by
James W. MacDonald
68k • written 29 days ago by
luna.picello
• 0
0
votes
1
reply
468
views
MEDIPS.meth gives table with NA rpkm values
MEDIPS
updated 4 weeks ago by
James W. MacDonald
68k • written 4 weeks ago by
huangdcc
• 0
0
votes
1
reply
807
views
Using offset in edgeR
edgeR
updated 4 weeks ago by
Gordon Smyth
52k • written 4 weeks ago by
mmadrzyk
• 0
2
votes
2
replies
1.7k
views
ExperimentHub full metadata
ExperimentHub
written 7 weeks ago by
igor
▴ 50
1
vote
2
replies
2.3k
views
Non-monotonic voomByGroup plot in Xenium data
XeniumIO
voom
5 weeks ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
0
replies
111
views
Guidance Requested on GCN Network Analysis and Module Enrichment in R
BioNERO
Bioconductor
Arabidopsis_thaliana_Data
updated 6 days ago by
Michael Love
43k • written 5 weeks ago by
Sabina
• 0
0
votes
1
reply
535
views
cytolib uses outdated boost call
cytolib
updated 5 weeks ago by
James W. MacDonald
68k • written 5 weeks ago by
machne
• 0
4
votes
8
replies
1.6k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2
edgeR
limma
xenium
Voom
5 weeks ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
2
replies
223
views
can't post
devel
updated 5 weeks ago by
shepherl
4.2k • written 5 weeks ago by
machne
• 0
0
votes
2
replies
311
views
HMP_2019_t2d data origin
curatedMetagenomicData
5 weeks ago
Blan
• 0
7
votes
9
replies
5.3k
views
competitive enrichment test yields too few significant results, self-contained too many
limma
DESeq2
fry
edgeR
5 weeks ago
bbao
▴ 10
0
votes
1
reply
1.2k
views
How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray
limma
BRAIN
Microarray
limma
BRAIN
updated 5 weeks ago by
Gordon Smyth
52k • written 16.5 years ago by
Dmitriy Verkhoturov
▴ 10
1,000 results • Page
1 of 20
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Replies
Comment: Updated Support Site Editor
by
vs
• 0
Thanks for posting this comment, I had the same issue and was able to solve it with the ASCII clue. I am a non-native speaker of English, a…
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
by
ATpoint
★ 4.9k
No, cells from the same donor are correlated due to the donor effect. There is literature on this you should read to get started. https:/…
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
by
Raya
• 0
Wouldn't each sample in the single cell rna seq act as a biological replicate? each condition (eg: mab3_20C) has ~70 single cell samples.
Comment: Getting way too many DEGs with LRT for time-series RNA-seq!
by
James W. MacDonald
68k
>Sequential post-exposure measurements of the same set of genes is not the same thing as having multiple treated groups! They are not the…
Comment: Getting way too many DEGs with LRT for time-series RNA-seq!
by
Denise
• 0
Sequential post-exposure measurements of the same set of genes is not the same thing as having multiple treated groups! And I suppose ther…
Votes
Comment: Updated Support Site Editor
Updated Support Site Editor
Comment: Updated Support Site Editor
Comment: DESeq2 used with zinbwave weights - Differences on contrasts calculations
Comment: DESeq2 used with zinbwave weights - Differences on contrasts calculations
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