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News:
Bioconductor 3.22 Release Schedule
Devel
Release
Bioconductor
written 4 months ago by
shepherl
4.3k
1
vote
11
replies
7.8k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
written 2.8 years ago by
Oscar
▴ 10
0
votes
2
replies
480
views
Help with defining groups
limpa
updated 19 days ago by
Gordon Smyth
53k • written 4 months ago by
Phinney, Brett
▴ 10
1
vote
2
replies
389
views
Error Loading Experiment from SimBenchData Package
Bioconductor
4 months ago
ksankaran
• 0
2
votes
4
replies
565
views
DESeq2 interactions
DESeq2
updated 3 months ago by
Michael Love
43k • written 4 months ago by
Michael
• 0
0
votes
3
replies
423
views
Sharing a collection of datasets in ExperimentHub
Bioconductor
updated 4 months ago by
Aaron Lun
★ 29k • written 4 months ago by
Stephen Piccolo
▴ 600
0
votes
3
replies
1.6k
views
problem for finding soft power for constructing network in WGCNA algorithm
RNA-seq
WGCNA package
soft power
written 7.6 years ago by
modarzi
▴ 10
0
votes
6
replies
720
views
GO.db and others package Download failure
GO.db
Bioconductor
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
Skyler
• 0
0
votes
0
replies
7
views
Spam:
Best Rehab Center In India | Luxury, Alcohol & Mental Health Care
COSMIC.67
4 months ago
Best Rehab Center
0
2
votes
2
replies
379
views
replace cat with message in glmTreat when lfc = 0
edgeR
glmTreat
updated 4 months ago by
Gordon Smyth
53k • written 4 months ago by
oliverd
• 0
0
votes
1
reply
237
views
Job:
Research and Service Group Leader positions in AI in Biology at EMBL
Bioconductor
written 4 months ago by
Wolfgang Huber
★ 13k
0
votes
1
reply
260
views
Differential motif analysis
motifmatchr
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
Marek Gierlinski
▴ 30
0
votes
1
reply
349
views
News:
Ensembl 115 has been released!
ensembl
ensembldb
biomaRt
written 4 months ago by
Ensembl_Jorge
▴ 10
1
vote
3
replies
484
views
readDNAStringSet with non DNA characters
Biostrings
4 months ago
biomiha
▴ 20
0
votes
2
replies
323
views
readBam vs read_bam_insert_metrics
cfDNAPro
cfDNA
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
rtrivedi1
▴ 10
1
vote
3
replies
485
views
How to construct a BSgenome object from a custom genome assembly using BSgenomeForge?
BSgenome
BSgenomeForge
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
mat149
▴ 80
3
votes
14
replies
1.4k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave
DESeq2
written 6 months ago by
Aurélie
• 0
5
votes
13
replies
1.6k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma
RNASeq
scRNAseq
updated 4 months ago by
Gordon Smyth
53k • written 4 months ago by
abaed
• 0
0
votes
1
reply
3.3k
views
Job:
Postdoctoral Research Position in Cancer Genomics at Dana-Farber Cancer Institute/Harvard University
cancer
computational biology
rnaseq
chipseq
Job
written 11.3 years ago by
gcyuan
• 0
0
votes
3
replies
430
views
Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq
DESeq2
updated 4 months ago by
Michael Love
43k • written 5 months ago by
yongjie.wang
• 0
0
votes
1
reply
853
views
Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm
DESeq2
updated 4 months ago by
Michael Love
43k • written 5 months ago by
KS
• 0
0
votes
3
replies
304
views
A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::select()
org.Ss.eg.db
AnnotationDbi
written 5 months ago by
Adam Munhall
• 0
0
votes
4
replies
497
views
voomLmFit fitted log-CPM values
limma
edgeR
updated 5 months ago by
Gordon Smyth
53k • written 5 months ago by
Lina
▴ 10
1
vote
3
replies
422
views
ROAST compare results with complex design
limma
mroast
roast
CAMERA
written 5 months ago by
Jiahao Tian
• 0
0
votes
0
replies
6
views
Spam:
Exploring Robotic Hair Restoration Procedure
COSMIC.67
5 months ago
paseje6172
0
0
votes
0
replies
189
views
News:
Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment
SingleCell
SingleCellWorkflow
SingleCellData
5 months ago
Ludwig Geistlinger
▴ 80
3
votes
5
replies
1.2k
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 5 months ago by
James W. MacDonald
68k • written 5 months ago by
snijesh
▴ 200
0
votes
1
reply
423
views
News:
Bioconductor Board Nominations Open
TAB
Bioconductor
CAB
written 6 months ago by
shepherl
4.3k
2
votes
8
replies
821
views
Are voomByGroup and voomLmFit compatible?
limma
voomLmFit
voomByGroup
updated 5 months ago by
Gordon Smyth
53k • written 5 months ago by
richardallenfriedmanbrooklyn
▴ 30
0
votes
3
replies
1.3k
views
How to analyze Affy data, CEL files not available
affy
affy
written 19.0 years ago by
Bobby Prill
▴ 60
0
votes
5
replies
721
views
HMP_2019_t2d data origin
curatedMetagenomicData
updated 5 months ago by
Levi Waldron
★ 1.1k • written 6 months ago by
Blan
• 0
17
votes
45
replies
13k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 5 months ago by
James W. MacDonald
68k • written 6.5 years ago by
lim6432
▴ 60
3
votes
4
replies
8.5k
views
Calculation of module membership in WGCNA
WGCNA
RNA-seq
ModuleMembership
Network
Hub gene
written 5.5 years ago by
Arindam
▴ 80
0
votes
11
replies
797
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse
DESeq2
5 months ago
Denise
• 0
3
votes
4
replies
644
views
p-adjusted values in multiple comparisons
StatisticalMethod
limma
RnaSeqSampleSizeData
updated 4 months ago by
Josh
• 0 • written 5 months ago by
ocanorocabayera
• 0
2
votes
6
replies
680
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
5 months ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
3
replies
353
views
DESeq2 inconsistent fits depending on model design with interacting factors
des
DESeq2
written 5 months ago by
fedor.bezrukov
▴ 10
0
votes
2
replies
704
views
Job:
Job: Ensembl Genebuild Project Leader
JobPosting
ensembldb
written 7 months ago by
Aleena_Ensembl
▴ 30
1
vote
2
replies
308
views
The default value of 'abundanceCol'
tximportData
5 months ago
Jinghua
• 0
1
vote
2
replies
436
views
Testing KO vs WT at day4/day14 with interactions in edgeR
scRNAseq
updated 5 months ago by
Gordon Smyth
53k • written 5 months ago by
Noah
• 0
2
votes
9
replies
1.1k
views
Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq
edgeR
LongRead
Transcript
5 months ago
mohammedtoufiq91
▴ 10
1
vote
2
replies
435
views
Difference between logFC in limma-voom and weighted limma-voom
limma
voom
weighting
5 months ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
11
replies
1.1k
views
emptyDrops new default alpha = Inf giving far fewer non-empty droplets than under old default of alpha = NULL
scrn
10x
scRNAseq
emptyDrops
DropletUtils
6 months ago • updated 5 months ago
Peter Hickey
▴ 760
0
votes
0
replies
6
views
Spam:
Chat GPT Gratuit
chipenrich
procoil
6 months ago
Lệ
0
3
votes
1
reply
504
views
Limpa Pipeline Order
limma
limpa
updated 6 months ago by
Gordon Smyth
53k • written 6 months ago by
abadgerw
• 0
3
votes
2
replies
496
views
Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
limma
updated 6 months ago by
Gordon Smyth
53k • written 6 months ago by
A.Barden
▴ 20
0
votes
8
replies
718
views
How to use limma to analyze complex temporal RNAseq data
timecourse
RNASeq
limma
6 months ago
Jiahao Tian
• 0
3
votes
7
replies
932
views
makeChipPackage(): Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows:
AnnotationForge
updated 5 months ago by
James W. MacDonald
68k • written 6 months ago by
Jaqueline
• 0
2
votes
2
replies
485
views
Limma : paired samples leading to unexpected estimates
limma
6 months ago
Basti
▴ 780
2
votes
2
replies
630
views
(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
6 months ago
sandmann.t
▴ 70
1,000 results • Page
4 of 20
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Comment: Questions about bacon QC and correction on EWAS results
by
Tikaaa2sahaaaq2c
• 0
In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Comment: using limma trend workflow in CAMERA
by
A.Barden
▴ 20
Do you need to set trend.var=TRUE when using camera in the limma-voom pipeline with RNA-Seq data (as apposed to limma-trend pipeline)?
Comment: Upcoming Ensembl API and data access changes - new blog post available
by
Tikaaa2sahaaaq2c
• 0
Just as the Ensembl team transitions to a new platform for streamlined data access, diners can benefit from a digital newks menu prices con…
Comment: Error message that there is no package called Biobase
by
DamionLedner99
• 0
thanks for sharing!!! https://cran.r-project.org/
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC
by
Ben
• 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Votes
Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
A: DESeq2 normalization vs VST vs rlog
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
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