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Views
Votes
2
votes
2
replies
390
views
Limma : paired samples leading to unexpected estimates
limma
3 months ago
Basti
▴ 780
2
votes
2
replies
462
views
(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
3 months ago
sandmann.t
▴ 70
0
votes
1
reply
188
views
muffz.plot2
Mfuzz
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
xiao
• 0
0
votes
2
replies
305
views
BiocManager::install() doesn't work
Install
Biocond
updated 3 months ago by
Marcel Ramos
700 • written 3 months ago by
flying_breadman
• 0
0
votes
4
replies
840
views
Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm
s-value
DESeq2
updated 3 months ago by
Michael Love
43k • written 3 months ago by
Erika
• 0
0
votes
1
reply
352
views
Feedback needed on new user-friendly BED file tool
bedbaser
offtopic
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
nadia
• 0
1
vote
2
replies
393
views
Differential expression on the transcript-level
DESeq2
updated 3 months ago by
swbarnes2
★ 1.4k • written 3 months ago by
泓朴
• 0
0
votes
0
replies
197
views
CRISPRSeek Question: changing weight and gRNA.size causes error
CRISPRseek
CRISPR
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
Citrus
• 0
0
votes
0
replies
177
views
Empty boxes in treemap plot rrvgo package
rrvgo
3 months ago
Asma
• 0
0
votes
3
replies
537
views
DEP R-package run_app ("TMT") spits this error: "Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'".
DEP
3 months ago
Shajahan
• 0
3
votes
13
replies
2.1k
views
Highly DE genes but small count difference within conditions
RNASeq
DESeq2
RNASeqData
written 13 months ago by
bioshot.com
• 0
3
votes
2
replies
859
views
Transcript expression analysis using EdgeR
edgeR
Transcript
RNASeq
3 months ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
215
views
Results with PON give more variants
mutect2
variants
pon
written 3 months ago by
ramiro.barrantes
▴ 10
0
votes
1
reply
257
views
ORFik: spliced 5utr regions
splicing
5utr
ORFik
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
luna.picello
• 0
0
votes
1
reply
587
views
MEDIPS.meth gives table with NA rpkm values
MEDIPS
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
huangdcc
• 0
0
votes
1
reply
920
views
Using offset in edgeR
edgeR
updated 3 months ago by
Gordon Smyth
53k • written 3 months ago by
mmadrzyk
• 0
2
votes
2
replies
1.9k
views
ExperimentHub full metadata
ExperimentHub
written 4 months ago by
igor
▴ 50
1
vote
2
replies
2.5k
views
Non-monotonic voomByGroup plot in Xenium data
XeniumIO
voom
3 months ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
0
replies
224
views
Guidance Requested on GCN Network Analysis and Module Enrichment in R
BioNERO
Bioconductor
Arabidopsis_thaliana_Data
updated 12 weeks ago by
Michael Love
43k • written 3 months ago by
Sabina
• 0
0
votes
1
reply
619
views
cytolib uses outdated boost call
cytolib
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
machne
• 0
4
votes
8
replies
1.8k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2
edgeR
limma
xenium
Voom
4 months ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
2
replies
323
views
can't post
devel
updated 4 months ago by
shepherl
4.2k • written 4 months ago by
machne
• 0
7
votes
9
replies
5.6k
views
competitive enrichment test yields too few significant results, self-contained too many
limma
DESeq2
fry
edgeR
4 months ago
bbao
▴ 10
0
votes
1
reply
1.4k
views
How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray
limma
BRAIN
Microarray
limma
BRAIN
updated 4 months ago by
Gordon Smyth
53k • written 16.8 years ago by
Dmitriy Verkhoturov
▴ 10
0
votes
2
replies
944
views
Install old version of DESeq2
apeglm
Install
DESeq2
version
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
Asma
• 0
0
votes
1
reply
505
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport
DESeq2
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
IUH
• 0
3
votes
9
replies
4.5k
views
Best practice for handling large data (matrix with >2^31-1 non-zero elements) in SingleCellExperiment?
SingleCellExperiment
updated 14 days ago by
dan.gatti
• 0 • written 4 months ago by
Fabian
▴ 10
0
votes
0
replies
251
views
Boolean Gate Combination for Any 2 Positive Events in flowWorkspace
flowWorkspace
FlowCytometry
4 months ago
Valeria
• 0
0
votes
0
replies
201
views
News:
Announcing a New Journal - Bioinformatics Methods and Applications - Now Open for Submissions
Bioconductor
4 months ago
Wei Shi
★ 3.6k
1
vote
3
replies
2.3k
views
Regarding the issue of background genes in enrichment analysis
KEGG
goTools
seqTools
written 4 months ago by
17506483572
▴ 10
0
votes
3
replies
2.3k
views
Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma
Bioconductor
Metabolomics
updated 4 months ago by
Gordon Smyth
53k • written 4 months ago by
anni
• 0
2
votes
4
replies
3.2k
views
I would like to perform differential expression analysis of lncRNAs using DESeq2 and edgeR.
diffGeneAnalysis
lncRNA
4 months ago
John
▴ 10
0
votes
2
replies
956
views
gene detection across experiments
DESeq2
Normalization
4 months ago
Mara
• 0
0
votes
3
replies
1.7k
views
RNA-seq: TPM batch effect correction
rnaseqDTU
Normalization
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
Samuel
• 0
1
vote
3
replies
1.7k
views
How can I correctly use phyloseq with Docker?
phylo
phyloseq
Docker
written 6 months ago by
Franz Bachmann
• 0
5
votes
11
replies
3.2k
views
parameters of filterByExpr
edgeR
DESeq2
filterByExpr
written 6 months ago by
caroline.zanchi
▴ 10
0
votes
5
replies
2.0k
views
compute_fasta_digest does not match Salmon index hash
tximeta
written 7 months ago by
Alex
• 0
0
votes
5
replies
845
views
WGCNA
WGCNA
Normalization
RNASeq
written 8 months ago by
Vishnu
• 0
3
votes
4
replies
5.2k
views
Analysis of clusters of a heatmap with enrichGO of clusterProfiler: choice fo the categories to visualize
clusterProfiler
enrichGO
ComplexHeatmap
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
caroline.zanchi
▴ 10
0
votes
3
replies
1.1k
views
TopGO question
topGO
top
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
Hannah
• 0
0
votes
2
replies
1.0k
views
Starting with a clean bioconductor rstudio container
Bioconductor
updated 4 months ago by
ATpoint
★ 5.0k • written 4 months ago by
Ramiro
• 0
0
votes
1
reply
2.4k
views
ChAMP pipeline error (champ.import)
software error
updated 4 months ago by
macdonaldfrench7286566
• 0 • written 6.6 years ago by
mhebba
• 0
0
votes
2
replies
540
views
Problem in Chip-seq data analysis using MACS3
chipseq
MACSdata
updated 4 months ago by
ATpoint
★ 5.0k • written 4 months ago by
Gaurav
• 0
1
vote
5
replies
4.2k
views
Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 3 months ago by
Michael Love
43k • written 5 months ago by
Alexander
• 0
0
votes
1
reply
701
views
Which GTF file to use for creation of tx2gene files?
tximport
updated 4 months ago by
Michael Love
43k • written 4 months ago by
Nicholas
• 0
1
vote
1
reply
2.2k
views
DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2
multifactorialdesign
interaction
InteractionSet
updated 4 months ago by
Michael Love
43k • written 4 months ago by
Integrative
• 0
0
votes
2
replies
1.1k
views
6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 4 months ago by
Michael Love
43k • written 4 months ago by
Rocio
• 0
0
votes
3
replies
959
views
Many transcripts missing from tx2gene created from Ensembl GTF file
kallisto
tximport
ensembl
updated 4 months ago by
Abbott
• 0 • written 4 months ago by
Nicholas
• 0
1
vote
2
replies
3.7k
views
Is voomByGroup available in limma?
limmaGUI
voom
4 months ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
4
replies
1.7k
views
How to use goana function with zebrafish genome from org.Dr.eg.db
org.Dr.eg.db
zebrafish
limma
4 months ago
Eric
• 0
46,666 results • Page
3 of 934
Recent ...
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Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
by
Matthew Thornton
▴ 380
WOW! Thank you so much for the information. I will do this.
Comment: "Watched Tags" are being erased rather than updated
by
RalphSavage99
• 0
Thanks for sharing https://github.com/Bioconductor/support.bioconductor.org/issues/112
Answer: Add additional maintainer for MOFA2
by
shepherl
4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
Answer: After running samtools, the featureCounts command crashed.
by
Kevin Blighe
★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot
by
Kevin Blighe
★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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to
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68k
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to
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▴ 40
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▴ 760
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