0
votes
3
replies
194
views
DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 5 weeks ago by ▴ 10
0
votes
2
replies
180
views
Create consensusMatrix for codon bases
Biostrings
updated 5 weeks ago by 68k • written 5 weeks ago by • 0
1
vote
1
reply
151
views
Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
updated 5 weeks ago by 53k • written 5 weeks ago by ▴ 10
0
votes
2
replies
558
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Job: Job: Ensembl Genebuild Project Leader
JobPosting ensembldb
written 3 months ago by ▴ 30
1
vote
2
replies
209
views
The default value of 'abundanceCol'
tximportData
6 weeks ago • updated 5 weeks ago Jinghua • 0
1
vote
2
replies
238
views
Testing KO vs WT at day4/day14 with interactions in edgeR
scRNAseq
updated 6 weeks ago by 53k • written 6 weeks ago by • 0
2
votes
9
replies
699
views
Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq edgeR LongRead Transcript
6 weeks ago • updated 5 weeks ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
230
views
Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
6 weeks ago richardallenfriedmanbrooklyn ▴ 30
0
votes
11
replies
779
views
emptyDrops new default alpha = Inf giving far fewer non-empty droplets than under old default of alpha = NULL
scrn 10x scRNAseq emptyDrops DropletUtils
6 weeks ago • updated 5 weeks ago Peter Hickey ▴ 760
0
votes
0
replies
115
views
Memory error while running alignments
DECIPHER Alignment
6 weeks ago Mihir • 0
0
votes
0
replies
6
views
Spam: Chat GPT Gratuit
chipenrich procoil
6 weeks ago Lệ 0
3
votes
1
reply
246
views
Limpa Pipeline Order
limma limpa
updated 6 weeks ago by 53k • written 6 weeks ago by • 0
2
votes
2
replies
303
views
Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
limma
updated 6 weeks ago by 53k • written 7 weeks ago by ▴ 10
0
votes
8
replies
499
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
7 weeks ago • updated 6 weeks ago Jiahao Tian • 0
3
votes
7
replies
581
views
makeChipPackage(): Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows:
AnnotationForge
updated 5 weeks ago by 68k • written 7 weeks ago by • 0
2
votes
2
replies
307
views
Limma : paired samples leading to unexpected estimates
limma
7 weeks ago Basti ▴ 780
2
votes
2
replies
305
views
(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
7 weeks ago sandmann.t ▴ 70
0
votes
1
reply
147
views
muffz.plot2
Mfuzz
updated 7 weeks ago by 68k • written 8 weeks ago by • 0
0
votes
2
replies
222
views
BiocManager::install() doesn't work
Install Biocond
updated 7 weeks ago by 700 • written 8 weeks ago by • 0
0
votes
4
replies
784
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Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 7 weeks ago by 43k • written 9 weeks ago by • 0
0
votes
1
reply
299
views
Feedback needed on new user-friendly BED file tool
bedbaser offtopic
updated 7 weeks ago by 68k • written 8 weeks ago by • 0
1
vote
2
replies
333
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Differential expression on the transcript-level
DESeq2
updated 8 weeks ago by ★ 1.4k • written 8 weeks ago by • 0
0
votes
0
replies
136
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CRISPRSeek Question: changing weight and gRNA.size causes error
CRISPRseek CRISPR
updated 8 weeks ago by 68k • written 8 weeks ago by • 0
0
votes
0
replies
119
views
Empty boxes in treemap plot rrvgo package
rrvgo
8 weeks ago Asma • 0
0
votes
3
replies
499
views
DEP R-package run_app ("TMT") spits this error: "Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'".
DEP
8 weeks ago • updated 6 weeks ago Shajahan • 0
3
votes
11
replies
1.9k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 11 months ago by • 0
3
votes
2
replies
780
views
Transcript expression analysis using EdgeR
edgeR Transcript RNASeq
8 weeks ago mohammedtoufiq91 ▴ 10
0
votes
0
replies
134
views
Results with PON give more variants
mutect2 variants pon
8 weeks ago ramiro.barrantes ▴ 10
0
votes
1
reply
208
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ORFik: spliced 5utr regions
splicing 5utr ORFik
updated 8 weeks ago by 68k • written 9 weeks ago by • 0
0
votes
1
reply
509
views
MEDIPS.meth gives table with NA rpkm values
MEDIPS
updated 9 weeks ago by 68k • written 9 weeks ago by • 0
0
votes
1
reply
865
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Using offset in edgeR
edgeR
updated 9 weeks ago by 53k • written 9 weeks ago by • 0
2
votes
2
replies
1.8k
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ExperimentHub full metadata
ExperimentHub
written 12 weeks ago by ▴ 50
1
vote
2
replies
2.4k
views
Non-monotonic voomByGroup plot in Xenium data
XeniumIO voom
9 weeks ago richardallenfriedmanbrooklyn ▴ 30
0
votes
0
replies
165
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Guidance Requested on GCN Network Analysis and Module Enrichment in R
BioNERO Bioconductor Arabidopsis_thaliana_Data
updated 5 weeks ago by 43k • written 9 weeks ago by • 0
0
votes
1
reply
579
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cytolib uses outdated boost call
cytolib
updated 9 weeks ago by 68k • written 9 weeks ago by • 0
4
votes
8
replies
1.7k
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Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
10 weeks ago • updated 9 weeks ago richardallenfriedmanbrooklyn ▴ 30
0
votes
2
replies
264
views
can't post
devel
updated 9 weeks ago by 4.2k • written 9 weeks ago by • 0
7
votes
9
replies
5.4k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
10 weeks ago • updated 9 weeks ago bbao ▴ 10
0
votes
1
reply
1.3k
views
How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray limma BRAIN Microarray limma BRAIN
updated 10 weeks ago by 53k • written 16.6 years ago by ▴ 10
0
votes
2
replies
904
views
Install old version of DESeq2
apeglm Install DESeq2 version
updated 10 weeks ago by 68k • written 10 weeks ago by • 0
0
votes
1
reply
435
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 10 weeks ago by 68k • written 10 weeks ago by • 0
3
votes
1
reply
4.0k
views
Best practice for handling large data (matrix with >2^31-1 non-zero elements) in SingleCellExperiment?
SingleCellExperiment
updated 10 weeks ago by ★ 29k • written 10 weeks ago by ▴ 10
0
votes
0
replies
141
views
Boolean Gate Combination for Any 2 Positive Events in flowWorkspace
flowWorkspace FlowCytometry
10 weeks ago Valeria • 0
0
votes
0
replies
151
views
News: Announcing a New Journal - Bioinformatics Methods and Applications - Now Open for Submissions
Bioconductor
10 weeks 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 11 weeks ago by ▴ 10
0
votes
3
replies
2.2k
views
Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma Bioconductor Metabolomics
updated 11 weeks ago by 53k • written 11 weeks ago by • 0
2
votes
4
replies
3.2k
views
I would like to perform differential expression analysis of lncRNAs using DESeq2 and edgeR.
diffGeneAnalysis lncRNA
11 weeks ago John ▴ 10
0
votes
2
replies
899
views
gene detection across experiments
DESeq2 Normalization
12 weeks ago Mara • 0
0
votes
3
replies
1.6k
views
RNA-seq: TPM batch effect correction
rnaseqDTU Normalization
updated 12 weeks ago by 68k • written 12 weeks ago by • 0
1
vote
3
replies
1.6k
views
How can I correctly use phyloseq with Docker?
phylo phyloseq Docker
written 4 months ago by • 0
46,635 results • Page 2 of 933
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Comment: EuroBioC2024 abstract submission is open! by leoblevins38 • 0
The difficulty of the game [Space Waves][1] gradually rises as it goes on. In order to help players become accustomed to the rhythm, early …
Answer: Sharing a collection of datasets in ExperimentHub by shepherl 4.2k
107 packages would be a lot! It is certainly possible (and recommended) to implement one package that utilizes ExperimentHub for controlli…
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Also, you never need to use anything but `BiocManager::install` to install any package, which has the beneficial side effect of ensuring th…
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Yes. Your packages have odd Y version numbers (where the version is X.Y.Z). That means they are devel packages (release versions have even …
Comment: GO.db and others package Download failure by Skyler • 0
Am I using Bioc-devel?
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Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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