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gene Set with high AUC score but no cells assigned to cell type
AUCell
9 weeks ago • updated 7 days ago
gogeni5529
• 0
0
votes
2
replies
259
views
featureCounts -L: high unassigned:mapq fraction
Bioconductor
written 8 weeks ago by
sikora
• 0
1
vote
2
replies
422
views
Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment
edgeR
miloR
Bioconductor
updated 22 days ago by
Kevin Blighe
★ 4.0k • written 8 weeks ago by
Joseph
• 0
1
vote
2
replies
366
views
incomplete imputation of missing values with LEA impute() function
Bioconductor
LEA
updated 22 days ago by
Kevin Blighe
★ 4.0k • written 8 weeks ago by
nadia
• 0
0
votes
2
replies
218
views
A problem occurs when running the monocle2
monocle
written 10 weeks ago by
yuheng_yang
• 0
5
votes
3
replies
387
views
Issues with downloading biomaRt - SeqInfo and S4 Vectors
S4Vectors
biomaRt
Seqinfo
updated 23 days ago by
James W. MacDonald
68k • written 23 days ago by
mgray20
▴ 10
1
vote
2
replies
197
views
News:
Important: Bioconductor Release 3.22 Delayed
release
written 4 weeks ago by
shepherl
4.2k
2
votes
2
replies
511
views
What R/Bioconductor tools would you recommend for the analysis of sncRNA, specifically piRNA?
Bioconductor
8 weeks ago • updated 20 days ago
Matthew Thornton
▴ 390
0
votes
2
replies
142
views
VariantAnnotation not does escape = within header string quotes
VariantAnnotation
updated 22 days ago by
Kevin Blighe
★ 4.0k • written 25 days ago by
Daniel Cameron
▴ 40
0
votes
2
replies
193
views
Setting up a DESeq2 Design with Paired Data
DESeq2
24 days ago • updated 23 days ago
Alexander
• 0
2
votes
2
replies
136
views
Suppress warning in RHDF5 write
rhdf5
24 days ago
nicolas.lhuillier
• 0
2
votes
2
replies
142
views
Failure to download resources (MeSHDb) from AnnotationHub
MeSHDb
AnnotationHub
25 days ago • updated 24 days ago
Steve Lianoglou
★ 13k
0
votes
3
replies
254
views
Integration: Paired-end vs healthy single-end from a different source
Bioconductor
written 27 days ago by
m.c.ruma
• 0
1
vote
4
replies
387
views
"Watched Tags" are being erased rather than updated
Bioconductor
updated 14 days ago by
RalphSavage99
• 0 • written 4 weeks ago by
jessica.anderson
▴ 10
0
votes
1
reply
217
views
Question about collapsing ASVs by genus level during DESeq2 analysis
Bioconductor
updated 26 days ago by
Michael Love
43k • written 7 weeks ago by
acharyapratiksha24
• 0
1
vote
2
replies
334
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 2.8 years ago by
Maria Doyle
▴ 110
0
votes
0
replies
12
views
Spam:
The Neon Code PolyTrack
Bioconductor
4 weeks ago
residentialplayt
0
2
votes
1
reply
159
views
News:
Bioconductor 3.22 Released!
release
Release
Bioconductor
Software
written 4 weeks ago by
shepherl
4.2k
0
votes
1
reply
248
views
News:
Save the Date for EuroBioC2026 in Turku!
Conference
written 4 weeks ago by
laurah ondari
• 0
0
votes
1
reply
131
views
News:
Save the Date: BioC2026
Bioconductor
written 4 weeks ago by
shepherl
4.2k
0
votes
1
reply
174
views
bake() and cool() resulting in an empty table
dar
updated 4 weeks ago by
Francesc
• 0 • written 4 weeks ago by
catherine.prattico
• 0
0
votes
3
replies
236
views
Using DESeq2 for age prediction
Bioconductor
updated 5 weeks ago by
ATpoint
★ 5.0k • written 5 weeks ago by
picasa1983
• 0
0
votes
4
replies
654
views
Issue with Soft-Thresholding in WGCNA
WGCNA
written 8 months ago by
Μαρία
• 0
4
votes
3
replies
596
views
DESeq2 for candidate gene analysis
Bioconductor
written 10 weeks ago by
piffelpaff
▴ 20
0
votes
1
reply
2.0k
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph
networkanalysis
Phylogenetics
phyloseq
updated 12 days ago by
Stefano Mangiola
▴ 40 • written 4.9 years ago by
Chantel
• 0
0
votes
3
replies
278
views
"organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames
Bioconductor
6 weeks ago
ubjw24
• 0
0
votes
3
replies
414
views
NA values for DESeq2 p-values and adjusted p-values using large sample sizes
Bioconductor
8 weeks ago • updated 6 weeks ago
Gabriel
• 0
0
votes
1
reply
152
views
Gatins Set error
flowCore
Bioconductor
updated 8 weeks ago by
James W. MacDonald
68k • written 8 weeks ago by
yoav.lubelsky
• 0
0
votes
1
reply
206
views
Job:
Senior Teaching Fellow (MSc Computational Biomedicine)
Bioconductor
updated 6 days ago by
eja.ger.m
• 0 • written 8 weeks ago by
s.samarajiwa
• 0
0
votes
1
reply
201
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq
variancePartition
RUVSeq
limma
edgeR
updated 7 weeks ago by
Gordon Smyth
53k • written 8 weeks ago by
ilaria.massaiu
• 0
0
votes
1
reply
350
views
News:
Bioconductor 3.22 Release Schedule
Devel
Release
Bioconductor
written 10 weeks ago by
shepherl
4.2k
1
vote
11
replies
7.2k
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
405
views
Help with defining groups
limpa
9 weeks ago • updated 7 weeks ago
Phinney, Brett
▴ 10
1
vote
2
replies
330
views
Error Loading Experiment from SimBenchData Package
Bioconductor
9 weeks ago • updated 7 weeks ago
ksankaran
• 0
2
votes
4
replies
464
views
DESeq2 interactions
DESeq2
updated 4 weeks ago by
Michael Love
43k • written 11 weeks ago by
Michael
• 0
0
votes
3
replies
333
views
Sharing a collection of datasets in ExperimentHub
Bioconductor
updated 8 weeks ago by
Aaron Lun
★ 29k • written 9 weeks ago by
Stephen Piccolo
▴ 600
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 7.4 years ago by
modarzi
▴ 10
0
votes
6
replies
476
views
GO.db and others package Download failure
GO.db
Bioconductor
updated 10 weeks ago by
James W. MacDonald
68k • written 10 weeks ago by
Skyler
• 0
0
votes
0
replies
7
views
Spam:
Best Rehab Center In India | Luxury, Alcohol & Mental Health Care
COSMIC.67
10 weeks ago
Best Rehab Center
0
2
votes
2
replies
285
views
replace cat with message in glmTreat when lfc = 0
edgeR
glmTreat
updated 10 weeks ago by
Gordon Smyth
53k • written 10 weeks ago by
oliverd
• 0
0
votes
1
reply
180
views
Job:
Research and Service Group Leader positions in AI in Biology at EMBL
Bioconductor
written 10 weeks ago by
Wolfgang Huber
★ 13k
0
votes
1
reply
162
views
Differential motif analysis
motifmatchr
updated 10 weeks ago by
James W. MacDonald
68k • written 10 weeks ago by
Marek Gierlinski
▴ 30
0
votes
1
reply
199
views
News:
Ensembl 115 has been released!
ensembl
ensembldb
biomaRt
written 10 weeks ago by
Ensembl_Jorge
• 0
1
vote
3
replies
406
views
readDNAStringSet with non DNA characters
Biostrings
11 weeks ago • updated 10 weeks ago
biomiha
▴ 20
0
votes
2
replies
266
views
readBam vs read_bam_insert_metrics
cfDNAPro
cfDNA
updated 10 weeks ago by
James W. MacDonald
68k • written 11 weeks ago by
rtrivedi1
▴ 10
1
vote
3
replies
397
views
How to construct a BSgenome object from a custom genome assembly using BSgenomeForge?
BSgenome
BSgenomeForge
updated 10 weeks ago by
James W. MacDonald
68k • written 11 weeks ago by
mat149
▴ 80
3
votes
14
replies
1.1k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave
DESeq2
written 4 months ago by
Aurélie
• 0
5
votes
13
replies
1.2k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma
RNASeq
scRNAseq
updated 9 weeks ago by
Gordon Smyth
53k • written 11 weeks ago by
abaed
• 0
0
votes
1
reply
3.2k
views
Job:
Postdoctoral Research Position in Cancer Genomics at Dana-Farber Cancer Institute/Harvard University
cancer
computational biology
rnaseq
chipseq
Job
written 11.1 years ago by
gcyuan
• 0
46,683 results • Page
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Comment: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR
by
efoss
▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma
by
Gordon Smyth
53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
• 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR
by
JKim
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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