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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
37 minutes ago • updated 34 minutes ago
colinmccornack
• 0
0
votes
0
replies
8
views
Post translational modifications and phosphoproteomics in limpa?
limpa
1 hour ago
james.eapen
• 0
0
votes
0
replies
34
views
MEFISTO: same GO term has plus NES in one time-decreasing factor and minus NES in another, how can that be?
MOFA2
1 day ago
Thomas
• 0
0
votes
0
replies
34
views
Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single Cell RNA Sequencing
scRNAseq
1 day ago
leixu0212
• 0
0
votes
1
reply
72
views
Add additional maintainer for MOFA2
MOFA2
updated 3 days ago by
shepherl
4.2k • written 3 days ago by
britta.velten
• 0
0
votes
2
replies
280
views
After running samtools, the featureCounts command crashed.
RNASeqData
Bioconductor
RNASeq
written 8 weeks ago by
Rui
• 0
0
votes
1
reply
378
views
Problem with the TMB plot
Bioconductor
updated 5 days ago by
Kevin Blighe
★ 4.0k • written 7 weeks ago by
nayanajose
• 0
0
votes
1
reply
274
views
gene Set with high AUC score but no cells assigned to cell type
AUCell
updated 5 days ago by
Kevin Blighe
★ 4.0k • written 7 weeks ago by
gogeni5529
• 0
0
votes
1
reply
192
views
featureCounts -L: high unassigned:mapq fraction
Bioconductor
updated 5 days ago by
Kevin Blighe
★ 4.0k • written 6 weeks ago by
sikora
• 0
1
vote
2
replies
387
views
Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment
edgeR
miloR
Bioconductor
updated 5 days ago by
Kevin Blighe
★ 4.0k • written 6 weeks ago by
Joseph
• 0
1
vote
2
replies
330
views
incomplete imputation of missing values with LEA impute() function
Bioconductor
LEA
updated 5 days ago by
Kevin Blighe
★ 4.0k • written 6 weeks ago by
nadia
• 0
0
votes
1
reply
151
views
A problem occurs when running the monocle2
monocle
updated 5 days ago by
Kevin Blighe
★ 4.0k • written 8 weeks ago by
yuheng_yang
• 0
0
votes
3
replies
128
views
Issues with downloading biomaRt - SeqInfo and S4 Vectors
S4Vectors
biomaRt
Seqinfo
updated 6 days ago by
James W. MacDonald
68k • written 6 days ago by
mgray20
• 0
1
vote
2
replies
182
views
News:
Important: Bioconductor Release 3.22 Delayed
release
written 16 days ago by
shepherl
4.2k
1
vote
2
replies
413
views
What R/Bioconductor tools would you recommend for the analysis of sncRNA, specifically piRNA?
Bioconductor
5 weeks ago • updated 2 days ago
Matthew Thornton
▴ 380
0
votes
2
replies
107
views
VariantAnnotation not does escape = within header string quotes
VariantAnnotation
updated 5 days ago by
Kevin Blighe
★ 4.0k • written 7 days ago by
Daniel Cameron
▴ 40
0
votes
2
replies
154
views
Setting up a DESeq2 Design with Paired Data
DESeq2
6 days ago
Alexander
• 0
2
votes
2
replies
110
views
Suppress warning in RHDF5 write
rhdf5
7 days ago
nicolas.lhuillier
• 0
2
votes
2
replies
108
views
Failure to download resources (MeSHDb) from AnnotationHub
MeSHDb
AnnotationHub
7 days ago • updated 6 days ago
Steve Lianoglou
★ 13k
0
votes
3
replies
227
views
Integration: Paired-end vs healthy single-end from a different source
Bioconductor
written 10 days ago by
m.c.ruma
• 0
1
vote
4
replies
337
views
"Watched Tags" are being erased rather than updated
Bioconductor
updated 2 days ago by
RalphSavage99
• 0 • written 14 days ago by
jessica.anderson
▴ 10
0
votes
1
reply
198
views
Question about collapsing ASVs by genus level during DESeq2 analysis
Bioconductor
updated 9 days ago by
Michael Love
43k • written 5 weeks ago by
acharyapratiksha24
• 0
1
vote
2
replies
311
views
Can limma be used with module eigengenes instead of genes?
limma
WGCNA
GSVA
written 3 months ago by
A.Barden
▴ 10
0
votes
7
replies
2.1k
views
News:
EuroBioC2023 abstract submission is open!
presentation
EuroBioC2023
Conference
community
Bioconductor
written 2.7 years ago by
Maria Doyle
▴ 100
0
votes
0
replies
12
views
Spam:
The Neon Code PolyTrack
Bioconductor
13 days ago
residentialplayt
0
2
votes
1
reply
145
views
News:
Bioconductor 3.22 Released!
release
Release
Bioconductor
Software
written 13 days ago by
shepherl
4.2k
0
votes
1
reply
173
views
News:
Save the Date for EuroBioC2026 in Turku!
Conference
written 15 days ago by
laurah ondari
• 0
0
votes
1
reply
118
views
News:
Save the Date: BioC2026
Bioconductor
written 16 days ago by
shepherl
4.2k
0
votes
1
reply
153
views
bake() and cool() resulting in an empty table
dar
updated 16 days ago by
Francesc
• 0 • written 16 days ago by
catherine.prattico
• 0
0
votes
3
replies
217
views
Using DESeq2 for age prediction
Bioconductor
updated 17 days ago by
ATpoint
★ 5.0k • written 19 days ago by
picasa1983
• 0
0
votes
4
replies
631
views
Issue with Soft-Thresholding in WGCNA
WGCNA
written 7 months ago by
Μαρία
• 0
4
votes
3
replies
550
views
DESeq2 for candidate gene analysis
Bioconductor
written 7 weeks ago by
piffelpaff
▴ 20
0
votes
2
replies
1.9k
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph
networkanalysis
Phylogenetics
phyloseq
written 4.8 years ago by
Chantel
• 0
2
votes
2
replies
393
views
DESeq2 design for haplotype MPRA
Bioconductor
4 weeks ago
Rita
• 0
0
votes
3
replies
258
views
"organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames
Bioconductor
4 weeks ago • updated 29 days ago
ubjw24
• 0
0
votes
3
replies
388
views
NA values for DESeq2 p-values and adjusted p-values using large sample sizes
Bioconductor
5 weeks ago • updated 28 days ago
Gabriel
• 0
0
votes
1
reply
142
views
Gatins Set error
flowCore
Bioconductor
updated 5 weeks ago by
James W. MacDonald
68k • written 5 weeks ago by
yoav.lubelsky
• 0
0
votes
1
reply
160
views
Job:
Senior Teaching Fellow (MSc Computational Biomedicine)
Bioconductor
written 5 weeks ago by
s.samarajiwa
• 0
0
votes
1
reply
181
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq
variancePartition
RUVSeq
limma
edgeR
updated 5 weeks ago by
Gordon Smyth
53k • written 6 weeks ago by
ilaria.massaiu
• 0
0
votes
0
replies
265
views
News:
Bioconductor 3.22 Release Schedule
Devel
Release
Bioconductor
8 weeks ago • updated 5 weeks ago
shepherl
4.2k
1
vote
11
replies
7.0k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
written 2.6 years ago by
Oscar
▴ 10
0
votes
2
replies
388
views
Help with defining groups
limpa
6 weeks ago • updated 5 weeks ago
Phinney, Brett
▴ 10
1
vote
2
replies
312
views
Error Loading Experiment from SimBenchData Package
Bioconductor
6 weeks ago • updated 5 weeks ago
ksankaran
• 0
2
votes
4
replies
441
views
DESeq2 interactions
DESeq2
updated 15 days ago by
Michael Love
43k • written 8 weeks ago by
Michael
• 0
0
votes
1
reply
198
views
GOseq Probability Weight Function bad fit
goseq
written 7 weeks ago by
francesca
• 0
0
votes
3
replies
313
views
Sharing a collection of datasets in ExperimentHub
Bioconductor
updated 6 weeks ago by
Aaron Lun
★ 29k • written 7 weeks ago by
Stephen Piccolo
▴ 600
0
votes
1
reply
198
views
Problem with viewGO(ref_path) in SpliceWiz
Bioconductor
SpliceWiz
7 weeks ago
jalte.jelsing
• 0
0
votes
3
replies
1.5k
views
problem for finding soft power for constructing network in WGCNA algorithm
RNA-seq
WGCNA package
soft power
written 7.3 years ago by
modarzi
▴ 10
0
votes
6
replies
448
views
GO.db and others package Download failure
GO.db
Bioconductor
updated 7 weeks ago by
James W. MacDonald
68k • written 8 weeks ago by
Skyler
• 0
0
votes
0
replies
7
views
Spam:
Best Rehab Center In India | Luxury, Alcohol & Mental Health Care
COSMIC.67
8 weeks ago
Best Rehab Center
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46,668 results • Page
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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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