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systemPipeR
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3
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2
replies
962
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How to export Slurm to my PATH in Ubuntu 20.04
systemPipeRdata
systempipeR
2.1 years ago
appropiate
• 0
0
votes
0
replies
497
views
Subdirectories created by systemPipeR
systemPipeRdata
systemPipeR
2.1 years ago
appropiate
• 0
0
votes
1
reply
746
views
how to analysis chip-seq data
systemPipeR
updated 2.3 years ago by
dcassol
▴ 100 • written 2.3 years ago by
Bioinformatics
▴ 30
2
votes
2
replies
2.9k
views
DiffBind installation fails: Error: package ‘BiocGenerics’ 0.34.0 is loaded, but >= 0.36.0 is required by ‘IRanges’
systemPipeR
Bioconductor
DiffBind
BiocGenerics
updated 3.2 years ago by
Martin Morgan
25k • written 3.2 years ago by
tina
• 0
0
votes
0
replies
668
views
Finding longest non overlapping open reading frames
predORF
systemPipeR
ORF
prediction
5.0 years ago
Mr.RB
▴ 20
14
votes
10
replies
3.6k
views
Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
systempiper
5.4 years ago
Deleted
▴ 70
0
votes
2
replies
1.2k
views
runCommandline error - bash: module: command not found
runCommandline
systemPipeR
bash
5.6 years ago
rj.innet
• 0
0
votes
2
replies
1.2k
views
Problem running (loading) systemPipeR package after downloading
systemPipeR
rnaseq
5.6 years ago
rj.innet
• 0
0
votes
2
replies
666
views
systemARGS not found
systempiper
5.7 years ago
kimberly.dickson
• 0
0
votes
3
replies
1.7k
views
error: NA counts not permitted
systempiper
edger
rna-seq
updated 6.0 years ago by
Aaron Lun
★ 28k • written 6.0 years ago by
clarisbaby
• 0
0
votes
1
reply
1.1k
views
What R version does systemPipeR runs
systempiper
R
batchjobs
updated 6.6 years ago by
Thomas Girke
★ 1.7k • written 6.6 years ago by
tarun2
• 0
0
votes
2
replies
1.2k
views
Why all of the logFC are NA in my edgeDF2
R
edger
systemPipeR
7.1 years ago
xuertowong
• 0
2
votes
3
replies
2.1k
views
SystemPipeR: alignments with ambiguous pairing were dumped.
R
rnaseq
tophat
summarizeoverlaps
systempiper
updated 7.4 years ago by
Thomas Girke
★ 1.7k • written 7.4 years ago by
abass.conteh
• 0
1
vote
2
replies
2.0k
views
Problem with systemPipeR package: run_edgeR or run_DESeq2 functions don't work
systempiper
run_edgeR
updated 7.5 years ago by
Thomas Girke
★ 1.7k • written 7.5 years ago by
alexandr.gopanenko
▴ 50
0
votes
7
replies
3.7k
views
DESeq2 LRT Error: less than one degree of freedom, perhaps full and reduced models are not in the correct order
deseq2
systempiper
Tutorial
7.8 years ago
musa
▴ 10
0
votes
4
replies
1.4k
views
SystemPipeR GO term enrichment analysis - filterDEG
systempiper
go term
7.9 years ago
A Gossner
▴ 50
0
votes
2
replies
1.6k
views
error when using seeFastqPlot
systempiper
seeFastqPlot
software error
ggplot2
geom_histogram
updated 8.2 years ago by
Thomas Girke
★ 1.7k • written 8.2 years ago by
setarosd
• 0
0
votes
4
replies
1.5k
views
systemPipeR with DESeq2
deseq2
systemPipeR
9.5 years ago
Ugo Borello
▴ 340
18 results • Page
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Comment: Estimating Cell Counts for EPIC V2 array data
by
normawiedman059
• 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Comment: Finding DEGs by using edgeR
by
Gordon Smyth
50k
Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
Comment: How to make DGEList and design matrix by edgeR package
by
prity6459
• 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR
by
prity6459
• 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
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A: Docker container with bioconductor and devtools
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
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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