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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
▴ 280
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 21 months ago by
Nikhil
• 0
0
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1
reply
900
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Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData
microbiome
offtopic
updated 2.8 years ago by
James W. MacDonald
65k • written 2.8 years ago by
gwagz8
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0
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3
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847
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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
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2
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789
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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
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1
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4
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679
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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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6 results • Page
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Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq
by
james.zhang20
• 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Comment: Deseq2 and Normalization of RNA sequencing data
by
ATpoint
★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
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A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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