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Comment: Comment: why is downloading the .tar.gz file for a given bioconductor package, then insta
18 months ago Ndimensional ▴ 20
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why is downloading the .tar.gz file for a given bioconductor package, then installing with R CMD INSTALL so much more effective than BiocManager::ins…
Bioconductor Install library biocmanager
updated 18 months ago by 6.7k • written 18 months ago by ▴ 20
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Comment: Comment: lfc direction of effect flipped for ashr, apeGLM, but accurate to biological dat
18 months ago Ndimensional ▴ 20
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4
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lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2 apeglm DESeq ApeGLM Ashr
updated 18 months ago by 43k • written 18 months ago by ▴ 20
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Comment: Comment: clinicalData() is not returning all columns from cBioPortal
19 months ago Ndimensional ▴ 20
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Comment: Comment: Importing RSEM processed data already formatted as a summarized experiment into
19 months ago Ndimensional ▴ 20
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1.8k
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Comment: Comment: Importing RSEM processed data already formatted as a summarized experiment into
19 months ago Ndimensional ▴ 20
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1.8k
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Comment: Comment: Importing RSEM processed data already formatted as a summarized experiment into
19 months ago Ndimensional ▴ 20
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1.8k
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Comment: Comment: Importing RSEM processed data already formatted as a summarized experiment into
19 months ago Ndimensional ▴ 20
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1.8k
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Comment: Comment: Importing RSEM processed data already formatted as a summarized experiment into
19 months ago Ndimensional ▴ 20
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1.8k
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Comment: Comment: Importing RSEM processed data already formatted as a summarized experiment into
19 months ago Ndimensional ▴ 20
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1.8k
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Comment: Comment: Importing RSEM processed data already formatted as a summarized experiment into
19 months ago Ndimensional ▴ 20
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Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
19 months ago Ndimensional ▴ 20
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863
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Comment: Comment: DESeq: relaxing gene filtering thresholds increases mean-Sd correlation, but rec
19 months ago Ndimensional ▴ 20
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Comment: Comment: Failure of beta estimates to converge in DESeq2 despite noncollinearity and reas
19 months ago Ndimensional ▴ 20
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3
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DESeq: relaxing gene filtering thresholds increases mean-Sd correlation, but recovers many important genes
metaanalysis meanSd genefilter DESeq2
19 months ago Ndimensional ▴ 20
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863
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Comment: Comment: DESeq: relaxing gene filtering thresholds increases mean-Sd correlation, but rec
19 months ago Ndimensional ▴ 20
2
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8
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1.5k
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Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge beta DESeq2
19 months ago Ndimensional ▴ 20
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0
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1.5k
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Answer: Answer: Failure of beta estimates to converge in DESeq2 despite noncollinearity and reas
19 months ago Ndimensional ▴ 20
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0
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1.5k
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Comment: Comment: Failure of beta estimates to converge in DESeq2 despite noncollinearity and reas
19 months ago Ndimensional ▴ 20
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1
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1.5k
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Comment: Comment: Failure of beta estimates to converge in DESeq2 despite noncollinearity and reas
19 months ago Ndimensional ▴ 20
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1
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869
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maEndtoEnd does not load on Mac version 3.6.0 or 3.6.2
maEndtoEnd
4.8 years ago Ndimensional ▴ 20
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976
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Comment: C: RNA-Seq analysis with DESeq2: showing two conditions do *not* significantly diff
4.9 years ago Ndimensional ▴ 20
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RNA-Seq analysis with DESeq2: showing two conditions do *not* significantly differ
deseq2 RNA-Seq uniform distribution data visualization
updated 4.9 years ago by ★ 13k • written 4.9 years ago by ▴ 20
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Using Effect Coding or Orthogonal Coding instead of dummy coding in DESeq2?
deseq2 multiple factor design interactions orthogonal coding effect coding
updated 7.2 years ago by ★ 3.0k • written 7.2 years ago by ▴ 20
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1.7k
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Comment: C: Please help me verify my compensation and spill matrices makes sense ( openCyto
7.3 years ago Ndimensional ▴ 20
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3
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1.7k
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Please help me verify my compensation and spill matrices makes sense ( openCyto package, in flowCore )
flow cytometry flowcore spillover compensation matrix
updated 7.3 years ago by ▴ 360 • written 7.3 years ago by ▴ 20
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