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Integration: Paired-end vs healthy single-end from a different source
Bioconductor
written 2 days ago by
m.c.ruma
• 0
1
vote
3
replies
211
views
"Watched Tags" are being erased rather than updated
Bioconductor
updated 1 day ago by
shepherl
4.2k • written 6 days ago by
jessica.anderson
▴ 10
0
votes
1
reply
146
views
Question about collapsing ASVs by genus level during DESeq2 analysis
Bioconductor
updated 1 day ago by
Michael Love
43k • written 28 days ago by
acharyapratiksha24
• 0
1
vote
2
replies
256
views
Can limma be used with module eigengenes instead of genes?
limma
WGCNA
GSVA
written 12 weeks ago by
A.Barden
▴ 10
0
votes
7
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2.0k
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News:
EuroBioC2023 abstract submission is open!
presentation
EuroBioC2023
Conference
community
Bioconductor
written 2.7 years ago by
Maria Doyle
▴ 100
0
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0
replies
11
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Spam:
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Bioconductor
5 days ago
residentialplayt
0
2
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1
reply
98
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News:
Bioconductor 3.22 Released!
release
Release
Bioconductor
Software
written 6 days ago by
shepherl
4.2k
0
votes
0
replies
77
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News:
Save the Date for EuroBioC2026 in Turku!
Conference
7 days ago
laurah ondari
• 0
1
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1
reply
106
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News:
Important: Bioconductor Release 3.22 Delayed
release
9 days ago • updated 8 days ago
shepherl
4.2k
0
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0
replies
46
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News:
Save the Date: BioC2026
Bioconductor
8 days ago
shepherl
4.2k
0
votes
1
reply
111
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bake() and cool() resulting in an empty table
dar
updated 8 days ago by
Francesc
• 0 • written 8 days ago by
catherine.prattico
• 0
0
votes
3
replies
165
views
Using DESeq2 for age prediction
Bioconductor
updated 9 days ago by
ATpoint
★ 5.0k • written 11 days ago by
picasa1983
• 0
0
votes
4
replies
585
views
Issue with Soft-Thresholding in WGCNA
WGCNA
written 7 months ago by
Μαρία
• 0
4
votes
3
replies
486
views
DESeq2 for candidate gene analysis
Bioconductor
written 6 weeks ago by
piffelpaff
▴ 20
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votes
2
replies
1.9k
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Co-occurrence Network Analysis between Algae and Bacteria
igraph
networkanalysis
Phylogenetics
phyloseq
written 4.8 years ago by
Chantel
• 0
1
vote
2
replies
222
views
DESeq2 design for haplotype MPRA
Bioconductor
22 days ago
Rita
• 0
0
votes
3
replies
222
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"organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames
Bioconductor
22 days ago
ubjw24
• 0
0
votes
3
replies
340
views
NA values for DESeq2 p-values and adjusted p-values using large sample sizes
Bioconductor
4 weeks ago • updated 21 days ago
Gabriel
• 0
0
votes
1
reply
106
views
Gatins Set error
flowCore
Bioconductor
updated 4 weeks ago by
James W. MacDonald
68k • written 4 weeks ago by
yoav.lubelsky
• 0
0
votes
1
reply
127
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Job:
Senior Teaching Fellow (MSc Computational Biomedicine)
Bioconductor
written 4 weeks ago by
s.samarajiwa
• 0
0
votes
1
reply
161
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What R/Bioconductor tools would you recommend for the analysis of sncRNA, specifically piRNA?
Bioconductor
written 4 weeks ago by
Matthew Thornton
▴ 380
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votes
1
reply
148
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq
variancePartition
RUVSeq
limma
edgeR
updated 29 days ago by
Gordon Smyth
53k • written 4 weeks ago by
ilaria.massaiu
• 0
0
votes
0
replies
196
views
News:
Bioconductor 3.22 Release Schedule
Devel
Release
Bioconductor
7 weeks ago • updated 4 weeks ago
shepherl
4.2k
1
vote
1
reply
233
views
incomplete imputation of missing values with LEA impute() function
Bioconductor
LEA
5 weeks ago • updated 4 weeks ago
nadia
• 0
1
vote
1
reply
295
views
Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment
edgeR
miloR
Bioconductor
updated 4 weeks ago by
ATpoint
★ 5.0k • written 5 weeks ago by
Joseph
• 0
0
votes
0
replies
101
views
featureCounts -L: high unassigned:mapq fraction
Bioconductor
updated 5 weeks ago by
James W. MacDonald
68k • written 5 weeks ago by
sikora
• 0
1
vote
11
replies
6.9k
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DiffBind - question on the use of filtered or unfiltered input data
DiffBind
written 2.5 years ago by
Oscar
▴ 10
0
votes
2
replies
352
views
Help with defining groups
limpa
5 weeks ago • updated 28 days ago
Phinney, Brett
▴ 10
1
vote
2
replies
281
views
Error Loading Experiment from SimBenchData Package
Bioconductor
5 weeks ago • updated 29 days ago
ksankaran
• 0
2
votes
4
replies
382
views
DESeq2 interactions
DESeq2
updated 7 days ago by
Michael Love
43k • written 7 weeks ago by
Michael
• 0
0
votes
1
reply
166
views
gene Set with high AUC score but no cells assigned to cell type
AUCell
written 6 weeks ago by
gogeni5529
• 0
0
votes
1
reply
160
views
GOseq Probability Weight Function bad fit
goseq
written 6 weeks ago by
francesca
• 0
0
votes
3
replies
275
views
Sharing a collection of datasets in ExperimentHub
Bioconductor
updated 5 weeks ago by
Aaron Lun
★ 29k • written 6 weeks ago by
Stephen Piccolo
▴ 600
0
votes
1
reply
158
views
Problem with viewGO(ref_path) in SpliceWiz
Bioconductor
SpliceWiz
6 weeks ago
jalte.jelsing
• 0
0
votes
1
reply
107
views
Problem with the TMB plot
Bioconductor
written 6 weeks ago by
nayanajose
• 0
0
votes
3
replies
1.4k
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
1
reply
159
views
After running samtools, the featureCounts command crashed.
RNASeqData
Bioconductor
RNASeq
written 7 weeks ago by
Rui
• 0
0
votes
6
replies
396
views
GO.db and others package Download failure
GO.db
Bioconductor
updated 6 weeks ago by
James W. MacDonald
68k • written 7 weeks ago by
Skyler
• 0
0
votes
0
replies
7
views
Spam:
Best Rehab Center In India | Luxury, Alcohol & Mental Health Care
COSMIC.67
7 weeks ago
Best Rehab Center
0
0
votes
2
replies
216
views
replace cat with message in glmTreat when lfc = 0
edgeR
glmTreat
updated 6 weeks ago by
Gordon Smyth
53k • written 7 weeks ago by
oliverd
• 0
0
votes
0
replies
98
views
Job:
Research and Service Group Leader positions in AI in Biology at EMBL
Bioconductor
7 weeks ago
Wolfgang Huber
★ 13k
0
votes
1
reply
115
views
Differential motif analysis
motifmatchr
updated 7 weeks ago by
James W. MacDonald
68k • written 7 weeks ago by
Marek Gierlinski
▴ 30
0
votes
0
replies
125
views
News:
Ensembl 115 has been released!
ensembl
ensembldb
biomaRt
7 weeks ago
Ensembl_Jorge
• 0
0
votes
0
replies
93
views
A problem occurs when running the monocle2
monocle
7 weeks ago
yuheng_yang
• 0
1
vote
3
replies
348
views
readDNAStringSet with non DNA characters
Biostrings
7 weeks ago
biomiha
▴ 20
0
votes
2
replies
216
views
readBam vs read_bam_insert_metrics
cfDNAPro
cfDNA
updated 7 weeks ago by
James W. MacDonald
68k • written 7 weeks ago by
rtrivedi1
▴ 10
1
vote
3
replies
350
views
How to construct a BSgenome object from a custom genome assembly using BSgenomeForge?
BSgenome
BSgenomeForge
updated 7 weeks ago by
James W. MacDonald
68k • written 7 weeks ago by
mat149
▴ 80
3
votes
14
replies
1.0k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave
DESeq2
written 3 months ago by
Aurélie
• 0
5
votes
13
replies
1.1k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma
RNASeq
scRNAseq
updated 6 weeks ago by
Gordon Smyth
53k • written 7 weeks ago by
abaed
• 0
0
votes
0
replies
169
views
Questions about pseudo counts from RUVSeq
RUVSeq
7 weeks ago
Yuxiang
• 0
1,000 results • Page
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Answer: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
This should now be resolved
Answer: Question about collapsing ASVs by genus level during DESeq2 analysis
by
Michael Love
43k
I'll just note that microbiome stats folks tend to use other tools than DESeq2. > several ASVs belong to the same genus but are not iden…
Answer: Integration: Paired-end vs healthy single-end from a different source
by
James W. MacDonald
68k
If by reprocess you mean generate libraries and re-sequence, then that's something you could do. Otherwise the biological and technical dif…
Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
we can investigate this issue. thank you for bringing it to our attention
Votes
Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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