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News:
BioC2023 abstract submission is now open!
presentation
BioC2023
Conference
community
Bioconductor
written 14 months ago by
Maria Doyle
▴ 70
0
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News:
EuroBioC2023 abstract submission closing soon!
presentation
EuroBioc2023
Conference
community
Bioconductor
12 months ago
Maria Doyle
▴ 70
0
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0
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456
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News:
EuroBioC2023 abstract submission is open!
presentation
EuroBioC2023
Conference
community
Bioconductor
14 months ago
Maria Doyle
▴ 70
1
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0
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887
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News:
Bioc2022 Submissions for talks, demos, workshops and poster now open! Deadline Tomorrow March 29!
presentation
Conference
bioc2022
2.3 years ago • updated 2.1 years ago
shepherl
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Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
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Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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