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DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq
SICER2
DiffBind
MACS2
offtopic
updated 2.9 years ago by
James W. MacDonald
65k • written 2.9 years ago by
Yuan Tian
▴ 270
1
vote
3
replies
1.1k
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Extract specific portion of a string and paste to a new column in R
Rscript
tidyr
dataframe
tidyverse
offtopic
updated 20 months ago by
Marcel Ramos
690 • written 20 months ago by
Nikhil
• 0
0
votes
1
reply
877
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Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData
microbiome
offtopic
updated 2.7 years ago by
James W. MacDonald
65k • written 2.7 years ago by
gwagz8
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0
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3
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829
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Why is RNA-Seq library size not constant among samples?
RNA-Seq
sequencer
library_size
sequency_depth
multiplexing
offtopic
updated 11 months ago by
James W. MacDonald
65k • written 11 months ago by
FedeXander
• 0
1
vote
2
replies
772
views
ERROR IN INSTALLATION PACKAGE IN R
derfinderData
SpikeInSubset
musicatk
Guitar
offtopic
updated 17 months ago by
Marcel Ramos
690 • written 17 months ago by
Chanchal
• 0
1
vote
4
replies
663
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Genomics data
mygene
offtopic
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
Shila
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Answer: FilterByExpr low counts with small sample size
by
Gordon Smyth
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It doesn't seem to me that there is necessarily any problem with the analysis. You that there are "too many low-reads" but actually there …
Answer: How to make DGEList and design matrix by edgeR package
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Gordon Smyth
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Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
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Gordon Smyth
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I am not clear what you mean that you have already normalized your data. How exactly did you normalize the data? The best way to do an edg…
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Gordon Smyth
50k
The log-cpm values from voom() are not free of batch effect. If you want batch-corrected log-cpm values, we recommend cpm() followed by rem…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
ATpoint
★ 4.0k
As expected normalization is **way** off, meaning in simple terms that the cloud is too high. The deep-blue area should be along y=0. Try t…
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Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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