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systempiper
•
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0
votes
4
replies
1.5k
views
systemPipeR with DESeq2
deseq2
systemPipeR
9.5 years ago
Ugo Borello
▴ 340
2
votes
3
replies
2.1k
views
SystemPipeR: alignments with ambiguous pairing were dumped.
R
rnaseq
tophat
summarizeoverlaps
systempiper
updated 7.5 years ago by
Thomas Girke
★ 1.7k • written 7.5 years ago by
abass.conteh
• 0
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
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
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
3
replies
1.7k
views
error: NA counts not permitted
systempiper
edger
rna-seq
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
clarisbaby
• 0
3
votes
2
replies
968
views
How to export Slurm to my PATH in Ubuntu 20.04
systemPipeRdata
systempipeR
2.1 years ago
appropiate
• 0
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
1.4k
views
SystemPipeR GO term enrichment analysis - filterDEG
systempiper
go term
7.9 years ago
A Gossner
▴ 50
0
votes
1
reply
750
views
how to analysis chip-seq data
systemPipeR
updated 2.3 years ago by
dcassol
▴ 100 • written 2.3 years ago by
Bioinformatics
▴ 30
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
1.2k
views
runCommandline error - bash: module: command not found
runCommandline
systemPipeR
bash
5.6 years ago
rj.innet
• 0
14
votes
10
replies
3.7k
views
Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
systempiper
5.4 years ago
Deleted
▴ 70
0
votes
0
replies
673
views
Finding longest non overlapping open reading frames
predORF
systemPipeR
ORF
prediction
5.0 years ago
Mr.RB
▴ 20
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
2
replies
1.2k
views
Why all of the logFC are NA in my edgeDF2
R
edger
systemPipeR
7.1 years ago
xuertowong
• 0
0
votes
0
replies
500
views
Subdirectories created by systemPipeR
systemPipeRdata
systemPipeR
2.1 years ago
appropiate
• 0
0
votes
2
replies
669
views
systemARGS not found
systempiper
5.7 years ago
kimberly.dickson
• 0
18 results • Page
1 of 1
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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…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Votes
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
Answer: How to retrieve gene ontology GO class from gene list?
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