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topaseq
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Running deprecated packages
ToPASeq
Deprecation
24 months ago
pgauthi1
• 0
0
votes
1
reply
700
views
SPIA function error in ToPASeq
topaseq
updated 5.9 years ago by
Gordon Smyth
50k • written 5.9 years ago by
Aditya Saxena
▴ 10
0
votes
0
replies
922
views
SPIA function error in ToPASeq
ToPASeq
SPIA
pathway analysis
R
6.1 years ago
fawazfebin
▴ 60
0
votes
1
reply
914
views
Problem in ToPASeq installation
topaseq
updated 6.5 years ago by
Martin Morgan
25k • written 6.5 years ago by
Aditya Saxena
▴ 10
0
votes
0
replies
1.6k
views
failed ToPASeq / igraph installation: file present, but not found
installation
package installation
topaseq
igraph
LD_LIBRARY_PATH
7.3 years ago
jan.soderman
• 0
0
votes
1
reply
847
views
Supplying ToPASeq a list of fold changes and their associated p-values
ToPASeq
updated 7.3 years ago by
theobroma22
▴ 10 • written 7.3 years ago by
rubi
▴ 110
1
vote
2
replies
1.3k
views
Normalized count or Count data for ToPASeq package
rnaseq
Topaseq
8.0 years ago
saamar.rajput
• 0
7 results • Page
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Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Votes
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
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