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graphite
•
reset
1
vote
3
replies
1.5k
views
graphite functions missing, installed version is out of date
graphite
bioclite
8.9 years ago
mhlinder
• 0
0
votes
3
replies
1.9k
views
runSPIA() in graphite package
Pathways
Breast
siggenes
PROcess
cycle
graphite
Pathways
Breast
siggenes
PROcess
cycle
updated 11.2 years ago by
Enrica
▴ 20 • written 11.2 years ago by
array chip
▴ 420
0
votes
4
replies
1.4k
views
graphite and PoTRa
graphite
potra
6.1 years ago
genomic8328
▴ 10
1
vote
2
replies
1.9k
views
Question on graphite/SPIA; extracting DE gene list
graphite
spia
runSPIA
updated 5.3 years ago by
Bioconductor Community
0 • written 9.1 years ago by
rgamini
• 0
1
vote
2
replies
1.6k
views
graphite KEGG pathway list vs KEGG pathway list
graphite
updated 9.1 years ago by
gabriele.sales
▴ 100 • written 9.1 years ago by
rgamini
• 0
0
votes
2
replies
1.1k
views
graphite package SSL certificate
graphite
2.4 years ago • updated 2.2 years ago
x
• 0
0
votes
11
replies
2.5k
views
"graphite" Biocarta 'native' graphs different from Biocarta web site?
Transcription
Pathways
Leukemia
graphite
Transcription
Pathways
Leukemia
graphite
11.9 years ago
Hamid Bolouri
▴ 90
0
votes
1
reply
1.7k
views
pathway analysis by SPIA using SPIA package vs graphite package
Pathways
SPIA
cycle
graphite
Pathways
SPIA
cycle
graphite
10.3 years ago
array chip
▴ 420
0
votes
2
replies
810
views
Direct interactions in graphite ?
graphite
interaction
updated 4.0 years ago by
gabriele.sales
▴ 100 • written 4.0 years ago by
emisecherre
• 0
0
votes
2
replies
1.3k
views
edge-less pathways in graphite
graphite
graphite
updated 12.0 years ago by
Paul Shannon
▴ 750 • written 12.0 years ago by
Hamid Bolouri
▴ 90
5
votes
4
replies
1.8k
views
Reactome pathways in ReactomeDB/graphite
reactomepa
reactome
graphite
updated 7.3 years ago by
gabriele.sales
▴ 100 • written 7.3 years ago by
i.sudbery
▴ 40
1
vote
2
replies
1.4k
views
KEGG data error?
bioconductor
graphite
pathway analysis
updated 7.2 years ago by
gabriele.sales
▴ 100 • written 7.2 years ago by
haoran.chen
• 0
1
vote
4
replies
1.5k
views
Indirect path in KEGG, activation or inhibition?
bioconductor
graphite
kegg
pathway analysis
updated 7.2 years ago by
gabriele.sales
▴ 100 • written 7.2 years ago by
haoran.chen
• 0
3
votes
2
replies
1.2k
views
Error installing graphite
graphite
updated 5.4 years ago by
gabriele.sales
▴ 100 • written 5.4 years ago by
Lluís Revilla Sancho
▴ 730
2
votes
3
replies
2.6k
views
Goseq analysis with Biocarta, Reactome, and NCI pathways?
goseq
graphite
9.2 years ago • updated 7.4 years ago
b.nota
▴ 360
0
votes
0
replies
1.2k
views
graphite biopax conversion code?
Pathways
graphite
Pathways
graphite
10.0 years ago
Ryan C. Thompson
★ 7.9k
16 results • Page
1 of 1
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Replies
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…
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…
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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