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News:
Upcoming Ensembl API and data access changes - new blog post available
ensembl
mart
biomaRt
ensembldb
5 hours ago
Ensembl_Jorge
▴ 10
0
votes
2
replies
85
views
problem reading bam files into nucleR
nucleR
updated 9 hours ago by
James W. MacDonald
68k • written 4 days ago by
efoss
▴ 10
0
votes
0
replies
11
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
15 hours ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
TOAST
15 hours ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
15 hours ago
Maya
0
0
votes
0
replies
8
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
15 hours ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
15 hours ago
Maya
0
3
votes
6
replies
448
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq
DESeq2
DifferentialExpression
RNASeqData
written 12 days ago by
Ahmed Salah
• 0
0
votes
1
reply
1.2k
views
two questions about limma
Microarray
limma
Microarray
limma
updated 2 days ago by
Gordon Smyth
53k • written 18.8 years ago by
De-Jian ZHAO
▴ 240
0
votes
1
reply
74
views
Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 2 days ago by
ATpoint
★ 5.0k • written 3 days ago by
Junmo
• 0
0
votes
0
replies
37
views
News:
EuroBioC2026 abstract submission is open!
Conference
Bioconductor
5 days ago
laurah ondari
• 0
0
votes
0
replies
54
views
PFAM formats changed - is it still possible to use this with ISA?
IsoformSwitchAnalyzeR
6 days ago
bolusharris
• 0
0
votes
0
replies
38
views
DECIPHER DesignProbes unable to design FISH-probes
decipher
FISH
DECIPHER
FISH-probe
probe-design
7 days ago
vreinmuth
• 0
0
votes
1
reply
1.1k
views
p.adjust BH Question
updated 7 days ago by
Gordon Smyth
53k • written 14.2 years ago by
David Young
▴ 10
1
vote
4
replies
252
views
Large logFC but somewhat high FDR
limpa
8 days ago • updated 3 hours ago
JKim
• 0
0
votes
0
replies
69
views
Job:
Bioinformatician at the Lausanne University Hospital
GenomicRanges
JobPosting
8 days ago
story.benjamin
▴ 20
3
votes
5
replies
296
views
upstream git branches of bioc-release
Bioconductor
written 8 days ago by
Jeroen
▴ 10
0
votes
2
replies
112
views
limpa - drivers for unusually high standard error?
limpa
updated 8 days ago by
Gordon Smyth
53k • written 8 days ago by
Julia Broadbent
• 0
1
vote
3
replies
1.8k
views
How can I correctly use phyloseq with Docker?
phylo
phyloseq
Docker
updated 10 days ago by
Kevin Blighe
★ 4.0k • written 7 months ago by
Franz Bachmann
• 0
0
votes
1
reply
364
views
Boolean Gate Combination for Any 2 Positive Events in flowWorkspace
flowWorkspace
FlowCytometry
updated 10 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Valeria
• 0
0
votes
2
replies
1.0k
views
Install old version of DESeq2
apeglm
Install
DESeq2
version
updated 10 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Asma
• 0
0
votes
1
reply
329
views
Guidance Requested on GCN Network Analysis and Module Enrichment in R
BioNERO
Bioconductor
Arabidopsis_thaliana_Data
updated 10 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Sabina
• 0
0
votes
2
replies
317
views
ORFik: spliced 5utr regions
splicing
5utr
ORFik
updated 10 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
luna.picello
• 0
0
votes
2
replies
360
views
BiocManager::install() doesn't work
Install
Biocond
updated 10 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
flying_breadman
• 0
0
votes
1
reply
283
views
Results with PON give more variants
mutect2
variants
pon
updated 10 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
ramiro.barrantes
▴ 10
0
votes
1
reply
237
views
Empty boxes in treemap plot rrvgo package
rrvgo
updated 10 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Asma
• 0
0
votes
1
reply
233
views
CRISPRSeek Question: changing weight and gRNA.size causes error
CRISPRseek
CRISPR
updated 10 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Citrus
• 0
0
votes
2
replies
407
views
Feedback needed on new user-friendly BED file tool
bedbaser
offtopic
updated 10 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
nadia
• 0
0
votes
1
reply
210
views
sigDF object in sesame
sesame
sesameData
updated 10 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Ramiro
• 0
0
votes
3
replies
325
views
Create consensusMatrix for codon bases
Biostrings
updated 10 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Hassan
• 0
0
votes
2
replies
404
views
Memory error while running alignments
DECIPHER
Alignment
updated 10 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Mihir
• 0
1
vote
11
replies
1.4k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2
scRNAseq
updated 10 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Raya
• 0
0
votes
1
reply
229
views
Finding duplicated entries in GRangesList
GenomicRanges
updated 11 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Marco
• 0
0
votes
1
reply
226
views
DESeq2 on non-RNASeq counts data
DESeq2
updated 11 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
vs
• 0
0
votes
2
replies
392
views
After running samtools, the featureCounts command crashed.
RNASeqData
Bioconductor
RNASeq
updated 1 day ago by
MarcHintz99
• 0 • written 10 weeks ago by
Rui
• 0
0
votes
1
reply
479
views
Problem with the TMB plot
Bioconductor
updated 11 days ago by
Kevin Blighe
★ 4.0k • written 10 weeks ago by
nayanajose
• 0
0
votes
1
reply
249
views
mzR-Rcpp compiler version issue
Rcpp
Perseus
mzR
updated 13 days ago by
Laurent Gatto
1.6k • written 3 months ago by
bniego
• 0
2
votes
3
replies
465
views
DESeq2 design for haplotype MPRA
Bioconductor
updated 12 days ago by
aimesd808
• 0 • written 7 weeks ago by
Rita
• 0
0
votes
1
reply
188
views
Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single Cell RNA Sequencing
scRNAseq
updated 13 days ago by
Kevin Blighe
★ 4.0k • written 21 days ago by
leixu0212
• 0
0
votes
0
replies
208
views
Corrupted SQLite while trying to install PANTHER.db?
SQLite
PANTHER.db
updated 13 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Alan
• 0
0
votes
0
replies
276
views
org.Ss.eg.db MAMDC4 maps to incorrect UNIPROT key
MAMDC4
org.Ss.eg.db
AnnotationDbi
updated 13 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Adam Munhall
• 0
0
votes
1
reply
270
views
Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment
singlecelle
scRNAseq
updated 13 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Francesco Silvestro
• 0
0
votes
1
reply
292
views
Extract snp information from genomic regions with biomaRt -> "oaries_snp"
biomaRt
updated 13 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Jesus
• 0
0
votes
2
replies
288
views
3-factor DESeq2 trime-series analysis
time-series
DESeq2
updated 13 days ago by
Kevin Blighe
★ 4.0k • written 11 weeks ago by
gogeni5529
• 0
0
votes
1
reply
250
views
Questions about pseudo counts from RUVSeq
RUVSeq
updated 13 days ago by
Kevin Blighe
★ 4.0k • written 11 weeks ago by
Yuxiang
• 0
0
votes
0
replies
246
views
Problem with viewGO(ref_path) in SpliceWiz
Bioconductor
SpliceWiz
updated 13 days ago by
Kevin Blighe
★ 4.0k • written 10 weeks ago by
jalte.jelsing
• 0
0
votes
0
replies
244
views
GOseq Probability Weight Function bad fit
goseq
updated 13 days ago by
Kevin Blighe
★ 4.0k • written 10 weeks ago by
francesca
• 0
0
votes
0
replies
93
views
[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 14 days ago by
Kevin Blighe
★ 4.0k • written 19 days ago by
colinmccornack
• 0
0
votes
2
replies
112
views
APAlyzer
APAlyzer
updated 14 days ago by
Kevin Blighe
★ 4.0k • written 15 days ago by
anjanaram1
▴ 10
2
votes
2
replies
237
views
Identifying differentially expressed genes in individual samples from a large cohort
limma
DifferentialExpression
14 days ago • updated 13 days ago
jamie.gearing
▴ 60
46,689 results • Page
1 of 934
Recent ...
Replies
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…
Answer: 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
Votes
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
Comment: upstream git branches of bioc-release
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Hervé Pagès
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▴ 30
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James W. MacDonald
68k
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4.2k
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