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0
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0
replies
13
views
Clarification on counting in Rsubread (featureCounts)
Rsubread
10 hours ago
Luca
• 0
0
votes
1
reply
71
views
NUPOP usage
TOAST
updated 4 days ago by
shepherl
4.2k • written 4 days ago by
Mohammad
• 0
1
vote
2
replies
258
views
News:
Important: Bioconductor Release 3.22 Delayed
release
written 7 weeks ago by
shepherl
4.2k
0
votes
1
reply
85
views
Question about RE-agnostic mode for intact Hi-C and Micro-C normalization(HiCDCPlus)
HiC
HiCDCPlus
written 6 days ago by
Chaoability
• 0
0
votes
2
replies
173
views
BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel
DESeq2
updated 10 days ago by
Michael Love
43k • written 11 days ago by
Benjamin
• 0
0
votes
1
reply
146
views
PTM analysis in LIMPA
limpa
updated 11 days ago by
Gordon Smyth
53k • written 11 days ago by
Diego FGR
• 0
1
vote
0
replies
149
views
News:
Upcoming Ensembl API and data access changes - new blog post available
ensembl
mart
biomaRt
ensembldb
13 days ago
Ensembl_Jorge
▴ 10
0
votes
2
replies
180
views
problem reading bam files into nucleR
nucleR
updated 13 days ago by
James W. MacDonald
68k • written 17 days ago by
efoss
▴ 10
0
votes
0
replies
13
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
13 days ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
TOAST
13 days ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
13 days ago
Maya
0
0
votes
0
replies
8
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
13 days ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
13 days ago
Maya
0
3
votes
6
replies
704
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq
DESeq2
DifferentialExpression
RNASeqData
written 25 days ago by
Ahmed Salah
• 0
0
votes
1
reply
1.2k
views
two questions about limma
Microarray
limma
Microarray
limma
updated 15 days ago by
Gordon Smyth
53k • written 18.8 years ago by
De-Jian ZHAO
▴ 240
0
votes
1
reply
137
views
Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 15 days ago by
ATpoint
★ 5.0k • written 16 days ago by
Junmo
• 0
0
votes
0
replies
71
views
News:
EuroBioC2026 abstract submission is open!
Conference
Bioconductor
18 days ago
laurah ondari
• 0
0
votes
0
replies
81
views
PFAM formats changed - is it still possible to use this with ISA?
IsoformSwitchAnalyzeR
19 days ago
bolusharris
• 0
0
votes
1
reply
151
views
DECIPHER DesignProbes unable to design FISH-probes
decipher
FISH
DECIPHER
FISH-probe
probe-design
updated 8 days ago by
Erik Wright
▴ 150 • written 20 days ago by
vreinmuth
• 0
0
votes
2
replies
1.2k
views
p.adjust BH Question
written 14.3 years ago by
David Young
▴ 10
1
vote
4
replies
341
views
Large logFC but somewhat high FDR
limpa
21 days ago • updated 13 days ago
JKim
• 0
0
votes
1
reply
148
views
Job:
Bioinformatician at the Lausanne University Hospital
GenomicRanges
JobPosting
written 21 days ago by
story.benjamin
▴ 20
3
votes
5
replies
430
views
upstream git branches of bioc-release
Bioconductor
written 21 days ago by
Jeroen
▴ 10
0
votes
2
replies
147
views
limpa - drivers for unusually high standard error?
limpa
updated 21 days ago by
Gordon Smyth
53k • written 21 days ago by
Julia Broadbent
• 0
1
vote
4
replies
1.9k
views
How can I correctly use phyloseq with Docker?
phylo
phyloseq
Docker
updated 2 days ago by
fnfgame
• 0 • written 7 months ago by
Franz Bachmann
• 0
0
votes
1
reply
397
views
Boolean Gate Combination for Any 2 Positive Events in flowWorkspace
flowWorkspace
FlowCytometry
updated 23 days ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
Valeria
• 0
0
votes
2
replies
1.1k
views
Install old version of DESeq2
apeglm
Install
DESeq2
version
updated 23 days ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
Asma
• 0
0
votes
1
reply
368
views
Guidance Requested on GCN Network Analysis and Module Enrichment in R
BioNERO
Bioconductor
Arabidopsis_thaliana_Data
updated 23 days ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
Sabina
• 0
0
votes
2
replies
352
views
ORFik: spliced 5utr regions
splicing
5utr
ORFik
updated 23 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
luna.picello
• 0
0
votes
2
replies
397
views
BiocManager::install() doesn't work
Install
Biocond
updated 23 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
flying_breadman
• 0
0
votes
2
replies
324
views
Results with PON give more variants
mutect2
variants
pon
written 4 months ago by
ramiro.barrantes
▴ 10
0
votes
1
reply
267
views
Empty boxes in treemap plot rrvgo package
rrvgo
updated 23 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Asma
• 0
0
votes
1
reply
264
views
CRISPRSeek Question: changing weight and gRNA.size causes error
CRISPRseek
CRISPR
updated 23 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Citrus
• 0
0
votes
2
replies
437
views
Feedback needed on new user-friendly BED file tool
bedbaser
offtopic
updated 23 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
nadia
• 0
0
votes
1
reply
245
views
sigDF object in sesame
sesame
sesameData
updated 23 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Ramiro
• 0
0
votes
3
replies
369
views
Create consensusMatrix for codon bases
Biostrings
updated 23 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Hassan
• 0
0
votes
2
replies
437
views
Memory error while running alignments
DECIPHER
Alignment
updated 23 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Mihir
• 0
1
vote
11
replies
1.6k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2
scRNAseq
updated 23 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Raya
• 0
0
votes
1
reply
263
views
Finding duplicated entries in GRangesList
GenomicRanges
updated 24 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Marco
• 0
0
votes
1
reply
258
views
DESeq2 on non-RNASeq counts data
DESeq2
updated 24 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
vs
• 0
0
votes
2
replies
442
views
After running samtools, the featureCounts command crashed.
RNASeqData
Bioconductor
RNASeq
updated 14 days ago by
MarcHintz99
• 0 • written 12 weeks ago by
Rui
• 0
0
votes
1
reply
508
views
Problem with the TMB plot
Bioconductor
updated 24 days ago by
Kevin Blighe
★ 4.0k • written 12 weeks ago by
nayanajose
• 0
0
votes
1
reply
281
views
mzR-Rcpp compiler version issue
Rcpp
Perseus
mzR
updated 26 days ago by
Laurent Gatto
1.6k • written 3 months ago by
bniego
• 0
2
votes
3
replies
506
views
DESeq2 design for haplotype MPRA
Bioconductor
written 8 weeks ago by
Rita
• 0
0
votes
1
reply
214
views
Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single Cell RNA Sequencing
scRNAseq
updated 26 days ago by
Kevin Blighe
★ 4.0k • written 4 weeks ago by
leixu0212
• 0
0
votes
0
replies
236
views
Corrupted SQLite while trying to install PANTHER.db?
SQLite
PANTHER.db
updated 26 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Alan
• 0
0
votes
1
reply
328
views
org.Ss.eg.db MAMDC4 maps to incorrect UNIPROT key
MAMDC4
org.Ss.eg.db
AnnotationDbi
written 3 months ago by
Adam Munhall
• 0
0
votes
1
reply
314
views
Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment
singlecelle
scRNAseq
updated 26 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Francesco Silvestro
• 0
0
votes
1
reply
329
views
Extract snp information from genomic regions with biomaRt -> "oaries_snp"
biomaRt
updated 26 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Jesus
• 0
0
votes
2
replies
327
views
3-factor DESeq2 trime-series analysis
time-series
DESeq2
updated 26 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
gogeni5529
• 0
1,000 results • Page
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Answer: NUPOP usage
by
shepherl
4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker?
by
fnfgame
• 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
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
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