0
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1
reply
169
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motifmatchr
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0
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1
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210
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News: Ensembl 115 has been released!
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readDNAStringSet with non DNA characters
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11 weeks ago biomiha ▴ 20
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273
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1
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3
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405
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How to construct a BSgenome object from a custom genome assembly using BSgenomeForge?
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DESeq2 used with zinbwave weights - Differences on contrasts calculations
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5
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13
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Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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3.2k
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Job: Postdoctoral Research Position in Cancer Genomics at Dana-Farber Cancer Institute/Harvard University
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0
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3
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367
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Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 12 weeks ago by 43k • written 3 months ago by • 0
0
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1
reply
691
views
Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
0
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3
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244
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A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::select()
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written 3 months ago by • 0
0
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4
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423
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voomLmFit fitted log-CPM values
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updated 3 months ago by 53k • written 3 months ago by ▴ 10
1
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3
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364
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ROAST compare results with complex design
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0
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Spam: Exploring Robotic Hair Restoration Procedure
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3 months ago paseje6172 0
0
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0
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News: Course: Single-cell analysis with R/Bioconductor
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3 months ago Ludwig Geistlinger ▴ 70
3
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5
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1.1k
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How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 3 months ago by 68k • written 3 months ago by ▴ 200
0
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1
reply
375
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News: Bioconductor Board Nominations Open
TAB Bioconductor CAB
written 4 months ago by 4.2k
2
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8
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726
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Are voomByGroup and voomLmFit compatible?
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updated 3 months ago by 53k • written 3 months ago by ▴ 30
0
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3
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How to analyze Affy data, CEL files not available
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5
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622
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HMP_2019_t2d data origin
curatedMetagenomicData
updated 3 months ago by ★ 1.1k • written 4 months ago by • 0
17
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45
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Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 3 months ago by 68k • written 6.4 years ago by ▴ 60
3
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4
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Calculation of module membership in WGCNA
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0
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11
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641
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Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
3 months ago Denise • 0
3
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4
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515
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p-adjusted values in multiple comparisons
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updated 11 weeks ago by • 0 • written 3 months ago by • 0
2
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6
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588
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Very different log2 Fold changes with DESeq2 and explict calculation
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3 months ago richardallenfriedmanbrooklyn ▴ 30
0
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3
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279
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2
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The default value of 'abundanceCol'
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4 months ago • updated 3 months ago Jinghua • 0
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2
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354
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updated 3 months ago by 53k • written 3 months ago by • 0
2
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9
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3 months ago mohammedtoufiq91 ▴ 10
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2
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372
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4 months ago • updated 3 months ago richardallenfriedmanbrooklyn ▴ 30
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11
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4 months ago • updated 3 months ago Peter Hickey ▴ 760
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0
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Limpa Pipeline Order
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updated 4 months ago by 53k • written 4 months ago by • 0
3
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2
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448
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Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
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updated 4 months ago by 53k • written 4 months ago by ▴ 10
0
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8
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635
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How to use limma to analyze complex temporal RNAseq data
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7
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738
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2
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2
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Limma : paired samples leading to unexpected estimates
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4 months ago Basti ▴ 780
2
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2
replies
515
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4 months ago sandmann.t ▴ 70
0
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1
reply
202
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muffz.plot2
Mfuzz
updated 4 months ago by 68k • written 4 months ago by • 0
0
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4
replies
880
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Using shrunken LFC and s-value from DESeq2 as DGE results
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updated 4 months ago by 43k • written 4 months ago by • 0
1
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2
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408
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Differential expression on the transcript-level
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updated 4 months ago by ★ 1.4k • written 4 months ago by • 0
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3
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553
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DEP R-package run_app ("TMT") spits this error: "Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'".
DEP
4 months ago Shajahan • 0
3
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13
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2.2k
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Highly DE genes but small count difference within conditions
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3
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2
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896
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Transcript expression analysis using EdgeR
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4 months ago mohammedtoufiq91 ▴ 10
0
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1
reply
604
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MEDIPS.meth gives table with NA rpkm values
MEDIPS
updated 4 months ago by 68k • written 4 months ago by • 0
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937
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Using offset in edgeR
edgeR
updated 4 months ago by 53k • written 4 months ago by • 0
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ExperimentHub full metadata
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2
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Non-monotonic voomByGroup plot in Xenium data
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4 months ago richardallenfriedmanbrooklyn ▴ 30
0
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1
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635
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cytolib uses outdated boost call
cytolib
updated 4 months ago by 68k • written 4 months ago by • 0
46,691 results • Page 3 of 934
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Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
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