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0
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2
replies
683
views
Problem with the TMB plot
Bioconductor
written 4 months ago by
nayanajose
• 0
0
votes
1
reply
359
views
mzR-Rcpp compiler version issue
Rcpp
Perseus
mzR
updated 11 weeks ago by
Laurent Gatto
1.6k • written 5 months ago by
bniego
• 0
2
votes
3
replies
609
views
DESeq2 design for haplotype MPRA
Bioconductor
written 3 months ago by
Rita
• 0
0
votes
1
reply
455
views
Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single Cell RNA Sequencing
scRNAseq
updated 11 weeks ago by
Kevin Blighe
★ 4.0k • written 12 weeks ago by
leixu0212
• 0
0
votes
0
replies
365
views
Corrupted SQLite while trying to install PANTHER.db?
SQLite
PANTHER.db
updated 11 weeks ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
Alan
• 0
0
votes
1
reply
450
views
org.Ss.eg.db MAMDC4 maps to incorrect UNIPROT key
MAMDC4
org.Ss.eg.db
AnnotationDbi
written 5 months ago by
Adam Munhall
• 0
0
votes
1
reply
373
views
Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment
singlecelle
scRNAseq
updated 11 weeks ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
Francesco Silvestro
• 0
0
votes
1
reply
410
views
Extract snp information from genomic regions with biomaRt -> "oaries_snp"
biomaRt
updated 11 weeks ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
Jesus
• 0
0
votes
2
replies
381
views
3-factor DESeq2 trime-series analysis
time-series
DESeq2
updated 11 weeks ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
gogeni5529
• 0
0
votes
1
reply
324
views
Questions about pseudo counts from RUVSeq
RUVSeq
updated 11 weeks ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Yuxiang
• 0
0
votes
0
replies
347
views
Problem with viewGO(ref_path) in SpliceWiz
Bioconductor
SpliceWiz
updated 11 weeks ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
jalte.jelsing
• 0
0
votes
1
reply
346
views
GOseq Probability Weight Function bad fit
goseq
written 4 months ago by
francesca
• 0
0
votes
0
replies
180
views
[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 11 weeks ago by
Kevin Blighe
★ 4.0k • written 11 weeks ago by
colinmccornack
• 0
0
votes
2
replies
193
views
APAlyzer
APAlyzer
updated 11 weeks ago by
Kevin Blighe
★ 4.0k • written 11 weeks ago by
anjanaram1
▴ 10
2
votes
2
replies
330
views
Identifying differentially expressed genes in individual samples from a large cohort
limma
DifferentialExpression
11 weeks ago
jamie.gearing
▴ 60
0
votes
2
replies
308
views
Alternative to BrainArray custom CDF packages for Affymetrix chips?
Bioconductor
updated 11 weeks ago by
Guido Hooiveld
★ 4.1k • written 11 weeks ago by
Stephen Piccolo
▴ 600
1
vote
2
replies
392
views
Error installing Seqinfo
Seqinfo
S4Vectors
updated 11 weeks ago by
shepherl
4.3k • written 11 weeks ago by
fabio.marroni
• 0
1
vote
0
replies
143
views
News:
Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
Bioconductor
11 weeks ago
Maria Doyle
▴ 110
0
votes
4
replies
311
views
Getting a large intercept with DESeq2
DESeq2
DifferentialExpression
TimeCourse
11 weeks ago
Denise
• 0
2
votes
2
replies
298
views
Post translational modifications and phosphoproteomics in limpa?
limpa
updated 19 days ago by
Gordon Smyth
53k • written 11 weeks ago by
james.eapen
• 0
0
votes
1
reply
163
views
Add additional maintainer for MOFA2
MOFA2
updated 12 weeks ago by
shepherl
4.3k • written 12 weeks ago by
britta.velten
• 0
1
vote
3
replies
708
views
gene Set with high AUC score but no cells assigned to cell type
AUCell
4 months ago • updated 10 weeks ago
gogeni5529
• 0
0
votes
2
replies
394
views
featureCounts -L: high unassigned:mapq fraction
Bioconductor
written 4 months ago by
sikora
• 0
1
vote
2
replies
510
views
Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment
edgeR
miloR
Bioconductor
updated 12 weeks ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Joseph
• 0
1
vote
2
replies
502
views
incomplete imputation of missing values with LEA impute() function
Bioconductor
LEA
updated 12 weeks ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
nadia
• 0
5
votes
3
replies
641
views
Issues with downloading biomaRt - SeqInfo and S4 Vectors
S4Vectors
biomaRt
Seqinfo
updated 12 weeks ago by
James W. MacDonald
68k • written 12 weeks ago by
mgray20
▴ 10
2
votes
2
replies
646
views
What R/Bioconductor tools would you recommend for the analysis of sncRNA, specifically piRNA?
Bioconductor
4 months ago • updated 12 weeks ago
Matthew Thornton
▴ 390
0
votes
2
replies
208
views
VariantAnnotation not does escape = within header string quotes
VariantAnnotation
updated 12 weeks ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Daniel Cameron
▴ 40
0
votes
2
replies
346
views
Setting up a DESeq2 Design with Paired Data
DESeq2
12 weeks ago
Alexander
• 0
2
votes
2
replies
194
views
Suppress warning in RHDF5 write
rhdf5
3 months ago
nicolas.lhuillier
• 0
2
votes
2
replies
237
views
Failure to download resources (MeSHDb) from AnnotationHub
MeSHDb
AnnotationHub
3 months ago • updated 12 weeks ago
Steve Lianoglou
★ 13k
0
votes
3
replies
325
views
Integration: Paired-end vs healthy single-end from a different source
Bioconductor
written 3 months ago by
m.c.ruma
• 0
1
vote
4
replies
476
views
"Watched Tags" are being erased rather than updated
Bioconductor
updated 11 weeks ago by
RalphSavage99
• 0 • written 3 months ago by
jessica.anderson
▴ 10
0
votes
1
reply
264
views
Question about collapsing ASVs by genus level during DESeq2 analysis
Bioconductor
updated 3 months ago by
Michael Love
43k • written 3 months ago by
acharyapratiksha24
• 0
1
vote
2
replies
413
views
Can limma be used with module eigengenes instead of genes?
limma
WGCNA
GSVA
written 5 months ago by
A.Barden
▴ 20
0
votes
7
replies
2.2k
views
News:
EuroBioC2023 abstract submission is open!
presentation
EuroBioC2023
Conference
community
Bioconductor
written 2.9 years ago by
Maria Doyle
▴ 110
0
votes
0
replies
12
views
Spam:
The Neon Code PolyTrack
Bioconductor
3 months ago
residentialplayt
0
2
votes
1
reply
717
views
News:
Bioconductor 3.22 Released!
release
Release
Bioconductor
Software
written 3 months ago by
shepherl
4.3k
0
votes
1
reply
442
views
News:
Save the Date for EuroBioC2026 in Turku!
Conference
written 3 months ago by
laurah ondari
• 0
0
votes
1
reply
571
views
News:
Save the Date: BioC2026
Bioconductor
written 3 months ago by
shepherl
4.3k
0
votes
1
reply
214
views
bake() and cool() resulting in an empty table
dar
updated 3 months ago by
Francesc
• 0 • written 3 months ago by
catherine.prattico
• 0
0
votes
3
replies
291
views
Using DESeq2 for age prediction
Bioconductor
updated 3 months ago by
ATpoint
★ 5.0k • written 3 months ago by
picasa1983
• 0
0
votes
4
replies
816
views
Issue with Soft-Thresholding in WGCNA
WGCNA
written 10 months ago by
Μαρία
• 0
4
votes
3
replies
657
views
DESeq2 for candidate gene analysis
Bioconductor
written 4 months ago by
piffelpaff
▴ 20
0
votes
1
reply
2.1k
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph
networkanalysis
Phylogenetics
phyloseq
updated 11 weeks ago by
Stefano Mangiola
▴ 40 • written 5.1 years ago by
Chantel
• 0
0
votes
3
replies
363
views
"organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames
Bioconductor
3 months ago
ubjw24
• 0
0
votes
3
replies
504
views
NA values for DESeq2 p-values and adjusted p-values using large sample sizes
Bioconductor
4 months ago • updated 3 months ago
Gabriel
• 0
0
votes
1
reply
206
views
Gatins Set error
flowCore
Bioconductor
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
yoav.lubelsky
• 0
0
votes
1
reply
274
views
Job:
Senior Teaching Fellow (MSc Computational Biomedicine)
Bioconductor
written 4 months ago by
s.samarajiwa
• 0
0
votes
1
reply
266
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq
variancePartition
RUVSeq
limma
edgeR
updated 4 months ago by
Gordon Smyth
53k • written 4 months ago by
ilaria.massaiu
• 0
1,000 results • Page
3 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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