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Question about RE-agnostic mode for intact Hi-C and Micro-C normalization(HiCDCPlus)
HiC
HiCDCPlus
36 minutes ago • updated 31 minutes ago
Chaoability
• 0
0
votes
2
replies
110
views
BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel
DESeq2
updated 3 days ago by
Michael Love
43k • written 5 days ago by
Benjamin
• 0
0
votes
1
reply
105
views
PTM analysis in LIMPA
limpa
updated 4 days ago by
Gordon Smyth
53k • written 4 days ago by
Diego FGR
• 0
1
vote
0
replies
117
views
News:
Upcoming Ensembl API and data access changes - new blog post available
ensembl
mart
biomaRt
ensembldb
6 days ago
Ensembl_Jorge
▴ 10
0
votes
2
replies
152
views
problem reading bam files into nucleR
nucleR
updated 6 days ago by
James W. MacDonald
68k • written 10 days ago by
efoss
▴ 10
0
votes
0
replies
13
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
7 days ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
TOAST
7 days ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
7 days ago
Maya
0
0
votes
0
replies
8
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
7 days ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
7 days ago
Maya
0
3
votes
6
replies
596
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq
DESeq2
DifferentialExpression
RNASeqData
written 18 days ago by
Ahmed Salah
• 0
0
votes
1
reply
1.2k
views
two questions about limma
Microarray
limma
Microarray
limma
updated 9 days ago by
Gordon Smyth
53k • written 18.8 years ago by
De-Jian ZHAO
▴ 240
0
votes
1
reply
114
views
Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 8 days ago by
ATpoint
★ 5.0k • written 9 days ago by
Junmo
• 0
0
votes
0
replies
52
views
News:
EuroBioC2026 abstract submission is open!
Conference
Bioconductor
11 days ago
laurah ondari
• 0
0
votes
0
replies
64
views
PFAM formats changed - is it still possible to use this with ISA?
IsoformSwitchAnalyzeR
13 days ago
bolusharris
• 0
0
votes
1
reply
90
views
DECIPHER DesignProbes unable to design FISH-probes
decipher
FISH
DECIPHER
FISH-probe
probe-design
updated 1 day ago by
Erik Wright
▴ 150 • written 14 days ago by
vreinmuth
• 0
0
votes
1
reply
1.1k
views
p.adjust BH Question
updated 14 days ago by
Gordon Smyth
53k • written 14.2 years ago by
David Young
▴ 10
1
vote
4
replies
290
views
Large logFC but somewhat high FDR
limpa
14 days ago • updated 6 days ago
JKim
• 0
0
votes
0
replies
83
views
Job:
Bioinformatician at the Lausanne University Hospital
GenomicRanges
JobPosting
14 days ago
story.benjamin
▴ 20
3
votes
5
replies
378
views
upstream git branches of bioc-release
Bioconductor
written 14 days ago by
Jeroen
▴ 10
0
votes
2
replies
131
views
limpa - drivers for unusually high standard error?
limpa
updated 15 days ago by
Gordon Smyth
53k • written 15 days ago by
Julia Broadbent
• 0
1
vote
4
replies
1.8k
views
How can I correctly use phyloseq with Docker?
phylo
phyloseq
Docker
written 7 months ago by
Franz Bachmann
• 0
0
votes
1
reply
376
views
Boolean Gate Combination for Any 2 Positive Events in flowWorkspace
flowWorkspace
FlowCytometry
updated 17 days ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
Valeria
• 0
0
votes
2
replies
1.0k
views
Install old version of DESeq2
apeglm
Install
DESeq2
version
updated 17 days ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
Asma
• 0
0
votes
1
reply
346
views
Guidance Requested on GCN Network Analysis and Module Enrichment in R
BioNERO
Bioconductor
Arabidopsis_thaliana_Data
updated 17 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Sabina
• 0
0
votes
2
replies
330
views
ORFik: spliced 5utr regions
splicing
5utr
ORFik
updated 17 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
luna.picello
• 0
0
votes
2
replies
373
views
BiocManager::install() doesn't work
Install
Biocond
updated 17 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
flying_breadman
• 0
0
votes
2
replies
303
views
Results with PON give more variants
mutect2
variants
pon
written 4 months ago by
ramiro.barrantes
▴ 10
0
votes
1
reply
249
views
Empty boxes in treemap plot rrvgo package
rrvgo
updated 17 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Asma
• 0
0
votes
1
reply
247
views
CRISPRSeek Question: changing weight and gRNA.size causes error
CRISPRseek
CRISPR
updated 17 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Citrus
• 0
0
votes
2
replies
420
views
Feedback needed on new user-friendly BED file tool
bedbaser
offtopic
updated 17 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
nadia
• 0
0
votes
1
reply
226
views
sigDF object in sesame
sesame
sesameData
updated 17 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Ramiro
• 0
0
votes
3
replies
340
views
Create consensusMatrix for codon bases
Biostrings
updated 17 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Hassan
• 0
0
votes
2
replies
417
views
Memory error while running alignments
DECIPHER
Alignment
updated 17 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Mihir
• 0
1
vote
11
replies
1.5k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2
scRNAseq
updated 17 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Raya
• 0
0
votes
1
reply
244
views
Finding duplicated entries in GRangesList
GenomicRanges
updated 18 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Marco
• 0
0
votes
1
reply
238
views
DESeq2 on non-RNASeq counts data
DESeq2
updated 18 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
vs
• 0
0
votes
2
replies
419
views
After running samtools, the featureCounts command crashed.
RNASeqData
Bioconductor
RNASeq
updated 8 days ago by
MarcHintz99
• 0 • written 11 weeks ago by
Rui
• 0
0
votes
1
reply
490
views
Problem with the TMB plot
Bioconductor
updated 18 days ago by
Kevin Blighe
★ 4.0k • written 11 weeks ago by
nayanajose
• 0
0
votes
1
reply
260
views
mzR-Rcpp compiler version issue
Rcpp
Perseus
mzR
updated 20 days ago by
Laurent Gatto
1.6k • written 3 months ago by
bniego
• 0
2
votes
3
replies
483
views
DESeq2 design for haplotype MPRA
Bioconductor
updated 19 days ago by
aimesd808
• 0 • written 7 weeks ago by
Rita
• 0
0
votes
1
reply
200
views
Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single Cell RNA Sequencing
scRNAseq
updated 20 days ago by
Kevin Blighe
★ 4.0k • written 27 days ago by
leixu0212
• 0
0
votes
0
replies
220
views
Corrupted SQLite while trying to install PANTHER.db?
SQLite
PANTHER.db
updated 20 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Alan
• 0
0
votes
1
reply
304
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
287
views
Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment
singlecelle
scRNAseq
updated 20 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Francesco Silvestro
• 0
0
votes
1
reply
307
views
Extract snp information from genomic regions with biomaRt -> "oaries_snp"
biomaRt
updated 20 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Jesus
• 0
0
votes
2
replies
300
views
3-factor DESeq2 trime-series analysis
time-series
DESeq2
updated 20 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
gogeni5529
• 0
0
votes
1
reply
257
views
Questions about pseudo counts from RUVSeq
RUVSeq
updated 20 days ago by
Kevin Blighe
★ 4.0k • written 12 weeks ago by
Yuxiang
• 0
0
votes
0
replies
254
views
Problem with viewGO(ref_path) in SpliceWiz
Bioconductor
SpliceWiz
updated 20 days ago by
Kevin Blighe
★ 4.0k • written 11 weeks ago by
jalte.jelsing
• 0
0
votes
1
reply
295
views
GOseq Probability Weight Function bad fit
goseq
written 11 weeks ago by
francesca
• 0
46,692 results • Page
1 of 934
Recent ...
Replies
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…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
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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