Bioconductor Plotly

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biocstyle plotly ggplot2

updated 8.1 years ago by Andrzej Oleś ▴ 750 • written 8.1 years ago by Lluís Revilla Sancho ▴ 760

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ChAMP Epigenetics plotly Shiny GUI News

8.8 years ago • updated 8.6 years ago Yuan Tian ▴ 90

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plotly R

updated 8.8 years ago by James W. MacDonald 68k • written 8.8 years ago by David ▴ 860

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Comment: emptyDrops new default alpha = Inf giving far fewer non-empty droplets than unde by Aaron Lun ★ 29k

See https://github.com/MarioniLab/DropletUtils/pull/125 for even more aggressive knee point detection, more cells, etc.

Comment: emptyDrops new default alpha = Inf giving far fewer non-empty droplets than unde by Peter Hickey ▴ 760

Sure: https://www.dropbox.com/scl/fi/8j4ztfh539oczvb1i0p1x/barcodeRanks.rds?rlkey=dwi7hjxtvw0kp7duve16zei9x&st=5pu3tq7o&dl=0

Comment: Create consensusMatrix for codon bases by James W. MacDonald 68k

Please note that the response was from a spam bot. They are getting pretty good at providing plausible sounding responses, but the goal isn…

Comment: emptyDrops new default alpha = Inf giving far fewer non-empty droplets than unde by Aaron Lun ★ 29k

Could you share the output of `barcodeRanks()`? I'd like to continue fiddling with the knee point detection.

Comment: makeChipPackage(): Error in data.frame(..., check.names = FALSE) : arguments by James W. MacDonald 68k

Glad I could help!

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Comment: Transcript expression analysis in edgeR from gtf file obtained from merging long

Comment: makeChipPackage(): Error in data.frame(..., check.names = FALSE) : arguments

Answer: Can limma be used with module eigengenes instead of genes?

Answer: The default value of 'abundanceCol'

Answer: Testing KO vs WT at day4/day14 with interactions in edgeR

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