0
votes
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
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2
replies
208
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3-factor DESeq2 trime-series analysis
time-series DESeq2
8 weeks ago • updated 7 weeks ago gogeni5529 • 0
0
votes
3
replies
321
views
Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 7 weeks ago by 43k • written 9 weeks ago by • 0
0
votes
1
reply
628
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
205
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A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::select()
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written 9 weeks ago by • 0
0
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4
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388
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voomLmFit fitted log-CPM values
limma edgeR
updated 8 weeks ago by 53k • written 8 weeks ago by ▴ 10
0
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0
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162
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Extract snp information from genomic regions with biomaRt -> "oaries_snp"
biomaRt
updated 9 weeks ago by 68k • written 9 weeks ago by • 0
1
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3
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325
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ROAST compare results with complex design
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written 9 weeks ago by • 0
0
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0
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5
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Spam: Exploring Robotic Hair Restoration Procedure
COSMIC.67
9 weeks ago paseje6172 0
0
votes
1
reply
175
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Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
9 weeks ago • updated 8 weeks ago Francesco Silvestro • 0
0
votes
0
replies
126
views
News: Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment SingleCell SingleCellWorkflow SingleCellData
9 weeks ago Ludwig Geistlinger ▴ 70
3
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5
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1.0k
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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
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1
reply
348
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News: Bioconductor Board Nominations Open
TAB Bioconductor CAB
written 3 months ago by 4.2k
2
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8
replies
671
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Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 9 weeks ago by 53k • written 11 weeks ago by ▴ 30
0
votes
3
replies
1.3k
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How to analyze Affy data, CEL files not available
affy affy
written 18.8 years ago by ▴ 60
0
votes
1
reply
204
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org.Ss.eg.db MAMDC4 maps to incorrect UNIPROT key
MAMDC4 org.Ss.eg.db AnnotationDbi
written 10 weeks ago by • 0
0
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0
replies
144
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mzR-Rcpp compiler version issue
Rcpp Perseus mzR
10 weeks ago bniego • 0
0
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0
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134
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Corrupted SQLite while trying to install PANTHER.db?
SQLite PANTHER.db
10 weeks ago Alan • 0
0
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5
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587
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HMP_2019_t2d data origin
curatedMetagenomicData
updated 10 weeks ago by ★ 1.1k • written 3 months ago by • 0
0
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0
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152
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Finding duplicated entries in GRangesList
GenomicRanges
10 weeks ago Marco • 0
17
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45
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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
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144
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DESeq2 on non-RNASeq counts data
DESeq2
11 weeks ago vs • 0
0
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0
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137
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sigDF object in sesame
sesame sesameData
11 weeks ago Ramiro • 0
3
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4
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7.9k
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Calculation of module membership in WGCNA
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written 5.2 years ago by ▴ 80
1
vote
10
replies
1.1k
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Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 5 weeks ago by • 0 • written 11 weeks ago by • 0
0
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11
replies
574
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Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
11 weeks ago • updated 10 weeks ago Denise • 0
3
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4
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473
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p-adjusted values in multiple comparisons
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updated 7 weeks ago by • 0 • written 11 weeks ago by • 0
2
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6
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529
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Very different log2 Fold changes with DESeq2 and explict calculation
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11 weeks ago richardallenfriedmanbrooklyn ▴ 30
0
votes
3
replies
243
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DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 11 weeks ago by ▴ 10
0
votes
2
replies
241
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Create consensusMatrix for codon bases
Biostrings
updated 12 weeks ago by 68k • written 12 weeks ago by • 0
0
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2
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602
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Job: Job: Ensembl Genebuild Project Leader
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written 4 months ago by ▴ 30
1
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2
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238
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The default value of 'abundanceCol'
tximportData
12 weeks ago Jinghua • 0
1
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2
replies
321
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Testing KO vs WT at day4/day14 with interactions in edgeR
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updated 12 weeks ago by 53k • written 12 weeks ago by • 0
2
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9
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906
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Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
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12 weeks ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
330
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Difference between logFC in limma-voom and weighted limma-voom
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12 weeks ago richardallenfriedmanbrooklyn ▴ 30
0
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11
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876
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emptyDrops new default alpha = Inf giving far fewer non-empty droplets than under old default of alpha = NULL
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3 months ago • updated 11 weeks ago Peter Hickey ▴ 760
0
votes
1
reply
280
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Memory error while running alignments
DECIPHER Alignment
updated 20 days ago by ▴ 150 • written 3 months ago by • 0
0
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0
replies
6
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Spam: Chat GPT Gratuit
chipenrich procoil
3 months ago Lệ 0
3
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1
reply
317
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Limpa Pipeline Order
limma limpa
updated 3 months ago by 53k • written 3 months ago by • 0
3
votes
2
replies
413
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
588
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
3 months ago • updated 12 weeks ago Jiahao Tian • 0
3
votes
7
replies
671
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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
385
views
Limma : paired samples leading to unexpected estimates
limma
3 months ago Basti ▴ 780
2
votes
2
replies
427
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
183
views
muffz.plot2
Mfuzz
updated 3 months ago by 68k • written 3 months ago by • 0
0
votes
2
replies
299
views
BiocManager::install() doesn't work
Install Biocond
updated 3 months ago by 700 • written 3 months ago by • 0
0
votes
4
replies
834
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Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
0
votes
1
reply
346
views
Feedback needed on new user-friendly BED file tool
bedbaser offtopic
updated 3 months ago by 68k • written 3 months ago by • 0
1
vote
2
replies
387
views
Differential expression on the transcript-level
DESeq2
updated 3 months ago by ★ 1.4k • written 3 months ago by • 0
0
votes
0
replies
189
views
CRISPRSeek Question: changing weight and gRNA.size causes error
CRISPRseek CRISPR
updated 3 months ago by 68k • written 3 months ago by • 0
1,000 results • Page 2 of 20
Recent ...
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Answer: "Watched Tags" are being erased rather than updated by shepherl 4.2k
This should now be resolved
Answer: Question about collapsing ASVs by genus level during DESeq2 analysis by Michael Love 43k
I'll just note that microbiome stats folks tend to use other tools than DESeq2. > several ASVs belong to the same genus but are not iden…
Answer: Integration: Paired-end vs healthy single-end from a different source by James W. MacDonald 68k
If by reprocess you mean generate libraries and re-sequence, then that's something you could do. Otherwise the biological and technical dif…
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
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Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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