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3
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6
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416
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq
DESeq2
DifferentialExpression
RNASeqData
written 11 days ago by
Ahmed Salah
• 0
0
votes
1
reply
1.2k
views
two questions about limma
Microarray
limma
Microarray
limma
updated 1 day ago by
Gordon Smyth
53k • written 18.8 years ago by
De-Jian ZHAO
▴ 240
0
votes
1
reply
65
views
Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 1 day ago by
ATpoint
★ 5.0k • written 2 days ago by
Junmo
• 0
0
votes
1
reply
66
views
problem reading bam files into nucleR
nucleR
3 days ago • updated 1 day ago
efoss
▴ 10
0
votes
0
replies
29
views
News:
EuroBioC2026 abstract submission is open!
Conference
Bioconductor
4 days ago
laurah ondari
• 0
0
votes
0
replies
49
views
PFAM formats changed - is it still possible to use this with ISA?
IsoformSwitchAnalyzeR
5 days ago
bolusharris
• 0
0
votes
0
replies
37
views
DECIPHER DesignProbes unable to design FISH-probes
decipher
FISH
DECIPHER
FISH-probe
probe-design
6 days ago
vreinmuth
• 0
0
votes
1
reply
1.1k
views
p.adjust BH Question
updated 6 days ago by
Gordon Smyth
53k • written 14.2 years ago by
David Young
▴ 10
1
vote
4
replies
240
views
Large logFC but somewhat high FDR
limpa
7 days ago • updated 6 days ago
JKim
• 0
0
votes
0
replies
65
views
Job:
Bioinformatician at the Lausanne University Hospital
GenomicRanges
JobPosting
7 days ago
story.benjamin
▴ 20
3
votes
5
replies
289
views
upstream git branches of bioc-release
Bioconductor
written 7 days ago by
Jeroen
▴ 10
0
votes
2
replies
111
views
limpa - drivers for unusually high standard error?
limpa
updated 7 days ago by
Gordon Smyth
53k • written 7 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 9 days ago by
Kevin Blighe
★ 4.0k • written 7 months ago by
Franz Bachmann
• 0
0
votes
1
reply
363
views
Boolean Gate Combination for Any 2 Positive Events in flowWorkspace
flowWorkspace
FlowCytometry
updated 9 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 9 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Asma
• 0
0
votes
1
reply
324
views
Guidance Requested on GCN Network Analysis and Module Enrichment in R
BioNERO
Bioconductor
Arabidopsis_thaliana_Data
updated 9 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Sabina
• 0
0
votes
2
replies
314
views
ORFik: spliced 5utr regions
splicing
5utr
ORFik
updated 9 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
luna.picello
• 0
0
votes
2
replies
356
views
BiocManager::install() doesn't work
Install
Biocond
updated 9 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
flying_breadman
• 0
0
votes
1
reply
281
views
Results with PON give more variants
mutect2
variants
pon
updated 9 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
ramiro.barrantes
▴ 10
0
votes
1
reply
235
views
Empty boxes in treemap plot rrvgo package
rrvgo
updated 9 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Asma
• 0
0
votes
1
reply
231
views
CRISPRSeek Question: changing weight and gRNA.size causes error
CRISPRseek
CRISPR
updated 9 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Citrus
• 0
0
votes
2
replies
401
views
Feedback needed on new user-friendly BED file tool
bedbaser
offtopic
updated 9 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
nadia
• 0
0
votes
1
reply
208
views
sigDF object in sesame
sesame
sesameData
updated 9 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Ramiro
• 0
0
votes
3
replies
323
views
Create consensusMatrix for codon bases
Biostrings
updated 9 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Hassan
• 0
0
votes
2
replies
400
views
Memory error while running alignments
DECIPHER
Alignment
updated 9 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 9 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Raya
• 0
0
votes
1
reply
227
views
Finding duplicated entries in GRangesList
GenomicRanges
updated 10 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Marco
• 0
0
votes
1
reply
223
views
DESeq2 on non-RNASeq counts data
DESeq2
updated 10 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
vs
• 0
0
votes
2
replies
391
views
After running samtools, the featureCounts command crashed.
RNASeqData
Bioconductor
RNASeq
updated 21 hours ago by
MarcHintz99
• 0 • written 10 weeks ago by
Rui
• 0
0
votes
1
reply
476
views
Problem with the TMB plot
Bioconductor
updated 10 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 12 days ago by
Laurent Gatto
1.6k • written 3 months ago by
bniego
• 0
2
votes
3
replies
464
views
DESeq2 design for haplotype MPRA
Bioconductor
updated 11 days ago by
aimesd808
• 0 • written 6 weeks ago by
Rita
• 0
0
votes
1
reply
187
views
Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single Cell RNA Sequencing
scRNAseq
updated 12 days ago by
Kevin Blighe
★ 4.0k • written 20 days ago by
leixu0212
• 0
0
votes
0
replies
208
views
Corrupted SQLite while trying to install PANTHER.db?
SQLite
PANTHER.db
updated 12 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Alan
• 0
0
votes
0
replies
275
views
org.Ss.eg.db MAMDC4 maps to incorrect UNIPROT key
MAMDC4
org.Ss.eg.db
AnnotationDbi
updated 12 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 12 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Francesco Silvestro
• 0
0
votes
1
reply
291
views
Extract snp information from genomic regions with biomaRt -> "oaries_snp"
biomaRt
updated 12 days ago by
Kevin Blighe
★ 4.0k • written 12 weeks ago by
Jesus
• 0
0
votes
2
replies
285
views
3-factor DESeq2 trime-series analysis
time-series
DESeq2
updated 12 days ago by
Kevin Blighe
★ 4.0k • written 11 weeks ago by
gogeni5529
• 0
0
votes
1
reply
248
views
Questions about pseudo counts from RUVSeq
RUVSeq
updated 12 days ago by
Kevin Blighe
★ 4.0k • written 11 weeks ago by
Yuxiang
• 0
0
votes
0
replies
245
views
Problem with viewGO(ref_path) in SpliceWiz
Bioconductor
SpliceWiz
updated 12 days ago by
Kevin Blighe
★ 4.0k • written 10 weeks ago by
jalte.jelsing
• 0
0
votes
0
replies
243
views
GOseq Probability Weight Function bad fit
goseq
updated 12 days ago by
Kevin Blighe
★ 4.0k • written 9 weeks ago by
francesca
• 0
0
votes
0
replies
93
views
[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 12 days ago by
Kevin Blighe
★ 4.0k • written 18 days ago by
colinmccornack
• 0
0
votes
2
replies
109
views
APAlyzer
APAlyzer
updated 12 days ago by
Kevin Blighe
★ 4.0k • written 14 days ago by
anjanaram1
▴ 10
2
votes
2
replies
234
views
Identifying differentially expressed genes in individual samples from a large cohort
limma
DifferentialExpression
13 days ago • updated 12 days ago
jamie.gearing
▴ 60
0
votes
2
replies
161
views
Alternative to BrainArray custom CDF packages for Affymetrix chips?
Bioconductor
updated 13 days ago by
Guido Hooiveld
★ 4.1k • written 17 days ago by
Stephen Piccolo
▴ 600
1
vote
2
replies
199
views
Error installing Seqinfo
Seqinfo
S4Vectors
updated 14 days ago by
shepherl
4.2k • written 16 days ago by
fabio.marroni
• 0
1
vote
0
replies
58
views
News:
Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
Bioconductor
17 days ago
Maria Doyle
▴ 110
0
votes
4
replies
182
views
Getting a large intercept with DESeq2
DESeq2
DifferentialExpression
TimeCourse
17 days ago • updated 14 days ago
Denise
• 0
2
votes
2
replies
167
views
Post translational modifications and phosphoproteomics in limpa?
limpa
18 days ago • updated 11 days ago
james.eapen
• 0
0
votes
1
reply
110
views
Add additional maintainer for MOFA2
MOFA2
updated 21 days ago by
shepherl
4.2k • written 21 days ago by
britta.velten
• 0
46,683 results • Page
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Replies
Comment: 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
Comment: Large logFC but somewhat high FDR
by
JKim
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
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
Comment: upstream git branches of bioc-release
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