0
votes
2
replies
250
views
readBam vs read_bam_insert_metrics
cfDNAPro cfDNA
updated 7 weeks ago by 68k • written 8 weeks ago by ▴ 10
1
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3
replies
374
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How to construct a BSgenome object from a custom genome assembly using BSgenomeForge?
BSgenome BSgenomeForge
updated 7 weeks ago by 68k • written 8 weeks ago by ▴ 80
3
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14
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1.1k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 3 months ago by • 0
5
votes
13
replies
1.2k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 6 weeks ago by 53k • written 8 weeks ago by • 0
0
votes
1
reply
196
views
Questions about pseudo counts from RUVSeq
RUVSeq
written 8 weeks ago by • 0
0
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1
reply
3.1k
views
Job: Postdoctoral Research Position in Cancer Genomics at Dana-Farber Cancer Institute/Harvard University
cancer computational biology rnaseq chipseq Job
written 11.0 years ago by • 0
0
votes
2
replies
220
views
3-factor DESeq2 trime-series analysis
time-series DESeq2
8 weeks ago gogeni5529 • 0
0
votes
3
replies
341
views
Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 8 weeks ago by 43k • written 9 weeks ago by • 0
0
votes
1
reply
643
views
Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm DESeq2
updated 8 weeks ago by 43k • written 10 weeks ago by • 0
0
votes
3
replies
212
views
A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::select()
org.Ss.eg.db AnnotationDbi
written 10 weeks ago by • 0
0
votes
4
replies
402
views
voomLmFit fitted log-CPM values
limma edgeR
updated 9 weeks ago by 53k • written 9 weeks ago by ▴ 10
0
votes
0
replies
167
views
Extract snp information from genomic regions with biomaRt -> "oaries_snp"
biomaRt
updated 9 weeks ago by 68k • written 9 weeks ago by • 0
1
vote
3
replies
341
views
ROAST compare results with complex design
limma mroast roast CAMERA
written 9 weeks ago by • 0
0
votes
0
replies
5
views
Spam: Exploring Robotic Hair Restoration Procedure
COSMIC.67
10 weeks ago paseje6172 0
0
votes
1
reply
181
views
Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
10 weeks ago • updated 9 weeks ago Francesco Silvestro • 0
0
votes
0
replies
129
views
News: Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment SingleCell SingleCellWorkflow SingleCellData
10 weeks ago Ludwig Geistlinger ▴ 70
3
votes
5
replies
1.1k
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 9 weeks ago by 68k • written 10 weeks ago by ▴ 200
0
votes
1
reply
352
views
News: Bioconductor Board Nominations Open
TAB Bioconductor CAB
written 3 months ago by 4.2k
2
votes
8
replies
687
views
Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 9 weeks ago by 53k • written 12 weeks ago by ▴ 30
0
votes
3
replies
1.3k
views
How to analyze Affy data, CEL files not available
affy affy
written 18.8 years ago by ▴ 60
0
votes
1
reply
206
views
org.Ss.eg.db MAMDC4 maps to incorrect UNIPROT key
MAMDC4 org.Ss.eg.db AnnotationDbi
written 11 weeks ago by • 0
0
votes
0
replies
150
views
mzR-Rcpp compiler version issue
Rcpp Perseus mzR
11 weeks ago bniego • 0
0
votes
0
replies
140
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Corrupted SQLite while trying to install PANTHER.db?
SQLite PANTHER.db
11 weeks ago Alan • 0
0
votes
5
replies
590
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HMP_2019_t2d data origin
curatedMetagenomicData
updated 11 weeks ago by ★ 1.1k • written 3 months ago by • 0
0
votes
0
replies
154
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Finding duplicated entries in GRangesList
GenomicRanges
11 weeks ago Marco • 0
17
votes
45
replies
13k
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Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 10 weeks ago by 68k • written 6.3 years ago by ▴ 60
0
votes
0
replies
147
views
DESeq2 on non-RNASeq counts data
DESeq2
11 weeks ago vs • 0
0
votes
0
replies
144
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sigDF object in sesame
sesame sesameData
11 weeks ago Ramiro • 0
3
votes
4
replies
8.0k
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Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
written 5.3 years ago by ▴ 80
1
vote
10
replies
1.1k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 6 weeks ago by • 0 • written 11 weeks ago by • 0
0
votes
11
replies
589
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
12 weeks ago • updated 11 weeks ago Denise • 0
3
votes
4
replies
478
views
p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 7 weeks ago by • 0 • written 12 weeks ago by • 0
2
votes
6
replies
539
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Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
12 weeks ago richardallenfriedmanbrooklyn ▴ 30
0
votes
3
replies
249
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DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 12 weeks ago by ▴ 10
0
votes
2
replies
245
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Create consensusMatrix for codon bases
Biostrings
updated 12 weeks ago by 68k • written 12 weeks ago by • 0
0
votes
2
replies
608
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Job: Job: Ensembl Genebuild Project Leader
JobPosting ensembldb
written 5 months ago by ▴ 30
1
vote
2
replies
242
views
The default value of 'abundanceCol'
tximportData
3 months ago • updated 12 weeks ago Jinghua • 0
1
vote
2
replies
328
views
Testing KO vs WT at day4/day14 with interactions in edgeR
scRNAseq
updated 3 months ago by 53k • written 3 months ago by • 0
2
votes
9
replies
920
views
Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
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3 months ago • updated 12 weeks ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
337
views
Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
3 months ago richardallenfriedmanbrooklyn ▴ 30
0
votes
11
replies
889
views
emptyDrops new default alpha = Inf giving far fewer non-empty droplets than under old default of alpha = NULL
scrn 10x scRNAseq emptyDrops DropletUtils
3 months ago • updated 12 weeks ago Peter Hickey ▴ 760
0
votes
1
reply
302
views
Memory error while running alignments
DECIPHER Alignment
updated 24 days ago by ▴ 150 • written 3 months ago by • 0
0
votes
0
replies
6
views
Spam: Chat GPT Gratuit
chipenrich procoil
3 months ago Lệ 0
3
votes
1
reply
323
views
Limpa Pipeline Order
limma limpa
updated 3 months ago by 53k • written 3 months ago by • 0
3
votes
2
replies
418
views
Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
limma
updated 3 months ago by 53k • written 3 months ago by ▴ 10
0
votes
8
replies
592
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
3 months ago Jiahao Tian • 0
3
votes
7
replies
687
views
makeChipPackage(): Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows:
AnnotationForge
updated 12 weeks ago by 68k • written 3 months ago by • 0
2
votes
2
replies
389
views
Limma : paired samples leading to unexpected estimates
limma
3 months ago Basti ▴ 780
2
votes
2
replies
448
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 68k • written 3 months ago by • 0
46,663 results • Page 2 of 934
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Comment: Save the Date: BioC2026 by eja.gsssssswwse.r.m • 0
Que notícia incrivel sobre o BioC2026 Para quem gosta de aproveitar o conteudo online, também e possvel Baixar [snaptube versão antiga][1] …
Comment: Ensembl 115 has been released! by eja.gsssssswwse.r.m • 0
Keeping up with Ensembls latest release ensures access to cutting-edge genomic information. For those balancing research and leisure, a mob…
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…
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
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Answer: DESeq2 design for haplotype MPRA
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Answer: Failure to download resources (MeSHDb) from AnnotationHub
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