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DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva
lfcshrink
DESeq2
10 weeks ago • updated 6 weeks ago
ja569116
• 0
0
votes
5
replies
3.2k
views
Ensembl site unresponsive via biomaRt
biomaRt
written 11 months ago by
hebda
• 0
0
votes
3
replies
371
views
segfault in edgeR glmQLFit
edgeR
updated 9 weeks ago by
Gordon Smyth
53k • written 10 weeks ago by
Mark
• 0
0
votes
4
replies
707
views
How does contrasts.fit do in limma to extract comparisons with a model having interaction terms?
limma
updated 7 weeks ago by
jtsy6383
• 0 • written 10 weeks ago by
Durian
• 0
0
votes
1
reply
365
views
News:
Opportunity to host EuroBioC2026 Preconference workshops!
Conference
Workshop
Bioconductor
written 10 weeks ago by
laurah ondari
• 0
0
votes
2
replies
246
views
NUPOP usage
TOAST
written 11 weeks ago by
Mohammad
• 0
1
vote
2
replies
485
views
News:
Important: Bioconductor Release 3.22 Delayed
release
written 4 months ago by
shepherl
4.3k
0
votes
1
reply
344
views
PTM analysis in LIMPA
limpa
updated 6 weeks ago by
Gordon Smyth
53k • written 12 weeks ago by
Diego FGR
• 0
1
vote
2
replies
532
views
News:
Upcoming Ensembl API and data access changes - new blog post available
ensembl
mart
biomaRt
ensembldb
written 12 weeks ago by
Ensembl_Jorge
▴ 10
0
votes
2
replies
366
views
problem reading bam files into nucleR
nucleR
updated 12 weeks ago by
James W. MacDonald
68k • written 3 months ago by
efoss
▴ 10
0
votes
0
replies
14
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
3 months ago
Maya
0
0
votes
0
replies
10
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
TOAST
3 months ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
3 months ago
Maya
0
0
votes
0
replies
8
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
3 months ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
3 months ago
Maya
0
3
votes
6
replies
1.1k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq
DESeq2
DifferentialExpression
RNASeqData
written 3 months ago by
Ahmed Salah
• 0
0
votes
1
reply
1.4k
views
two questions about limma
Microarray
limma
Microarray
limma
updated 3 months ago by
Gordon Smyth
53k • written 19.0 years ago by
De-Jian ZHAO
▴ 240
0
votes
1
reply
285
views
Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 3 months ago by
ATpoint
★ 5.0k • written 3 months ago by
Junmo
• 0
0
votes
1
reply
456
views
News:
EuroBioC2026 abstract submission is open!
Conference
Bioconductor
written 3 months ago by
laurah ondari
• 0
0
votes
1
reply
251
views
PFAM formats changed - is it still possible to use this with ISA?
IsoformSwitchAnalyzeR
written 3 months ago by
bolusharris
• 0
0
votes
3
replies
411
views
DECIPHER DesignProbes unable to design FISH-probes
decipher
FISH
DECIPHER
FISH-probe
probe-design
written 3 months ago by
vreinmuth
• 0
0
votes
2
replies
1.3k
views
p.adjust BH Question
written 14.5 years ago by
David Young
▴ 10
1
vote
4
replies
603
views
Large logFC but somewhat high FDR
limpa
3 months ago • updated 12 weeks ago
JKim
• 0
0
votes
1
reply
403
views
Job:
Bioinformatician at the Lausanne University Hospital
GenomicRanges
JobPosting
written 3 months ago by
story.benjamin
▴ 20
3
votes
5
replies
656
views
upstream git branches of bioc-release
Bioconductor
written 3 months ago by
Jeroen
▴ 10
0
votes
2
replies
360
views
limpa - drivers for unusually high standard error?
limpa
updated 3 months ago by
Gordon Smyth
53k • written 3 months ago by
Julia Broadbent
• 0
1
vote
4
replies
2.2k
views
How can I correctly use phyloseq with Docker?
phylo
phyloseq
Docker
updated 11 weeks ago by
fnfgame
• 0 • written 10 months ago by
Franz Bachmann
• 0
0
votes
2
replies
561
views
Boolean Gate Combination for Any 2 Positive Events in flowWorkspace
flowWorkspace
FlowCytometry
written 7 months ago by
Valeria
• 0
0
votes
2
replies
1.3k
views
Install old version of DESeq2
apeglm
Install
DESeq2
version
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 7 months ago by
Asma
• 0
0
votes
1
reply
506
views
Guidance Requested on GCN Network Analysis and Module Enrichment in R
BioNERO
Bioconductor
Arabidopsis_thaliana_Data
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 7 months ago by
Sabina
• 0
0
votes
2
replies
512
views
ORFik: spliced 5utr regions
splicing
5utr
ORFik
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 7 months ago by
luna.picello
• 0
0
votes
2
replies
924
views
BiocManager::install() doesn't work
Install
Biocond
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 7 months ago by
flying_breadman
• 0
0
votes
2
replies
534
views
Results with PON give more variants
mutect2
variants
pon
written 7 months ago by
ramiro.barrantes
▴ 10
0
votes
2
replies
494
views
Empty boxes in treemap plot rrvgo package
rrvgo
written 7 months ago by
Asma
• 0
0
votes
1
reply
384
views
CRISPRSeek Question: changing weight and gRNA.size causes error
CRISPRseek
CRISPR
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 7 months ago by
Citrus
• 0
0
votes
2
replies
711
views
Feedback needed on new user-friendly BED file tool
bedbaser
offtopic
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 7 months ago by
nadia
• 0
0
votes
1
reply
415
views
sigDF object in sesame
sesame
sesameData
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 6 months ago by
Ramiro
• 0
0
votes
3
replies
495
views
Create consensusMatrix for codon bases
Biostrings
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 6 months ago by
Hassan
• 0
0
votes
2
replies
546
views
Memory error while running alignments
DECIPHER
Alignment
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 6 months ago by
Mihir
• 0
1
vote
11
replies
2.6k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2
scRNAseq
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 6 months ago by
Raya
• 0
0
votes
1
reply
391
views
Finding duplicated entries in GRangesList
GenomicRanges
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 6 months ago by
Marco
• 0
0
votes
2
replies
454
views
DESeq2 on non-RNASeq counts data
DESeq2
written 6 months ago by
vs
• 0
0
votes
2
replies
647
views
After running samtools, the featureCounts command crashed.
RNASeqData
Bioconductor
RNASeq
updated 3 months ago by
MarcHintz99
• 0 • written 5 months ago by
Rui
• 0
0
votes
2
replies
751
views
Problem with the TMB plot
Bioconductor
written 5 months ago by
nayanajose
• 0
0
votes
1
reply
371
views
mzR-Rcpp compiler version issue
Rcpp
Perseus
mzR
updated 3 months ago by
Laurent Gatto
1.6k • written 6 months ago by
bniego
• 0
2
votes
3
replies
673
views
DESeq2 design for haplotype MPRA
Bioconductor
written 4 months ago by
Rita
• 0
0
votes
1
reply
636
views
Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single Cell RNA Sequencing
scRNAseq
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
leixu0212
• 0
0
votes
0
replies
418
views
Corrupted SQLite while trying to install PANTHER.db?
SQLite
PANTHER.db
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 6 months ago by
Alan
• 0
0
votes
1
reply
534
views
org.Ss.eg.db MAMDC4 maps to incorrect UNIPROT key
MAMDC4
org.Ss.eg.db
AnnotationDbi
written 6 months ago by
Adam Munhall
• 0
0
votes
1
reply
416
views
Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment
singlecelle
scRNAseq
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 6 months ago by
Francesco Silvestro
• 0
1,000 results • Page
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Answer: Inconsistencies between accessor functions for TxDb databases with selected seql
by
a2a2hd42aa
• 0
Technical inconsistencies in database accessors can disrupt your workflow, but finding a reliable source to download online mobile games sh…
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
by
A.Barden
▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions
by
Gordon Smyth
53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack
by
a2a2hd42aa
• 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
by
strawberry3
• 0
Hi, thank you all for the advice. Using James's advice, I managed to install SNPlocs.Hsapiens.dbSNP155.GRCh38, but it took almost half an …
Votes
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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