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Showing :
egsea
•
reset
9
votes
7
replies
20k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea
gsva
piano
egsea
updated 4 months ago by
amin8w
▴ 10 • written 6.8 years ago by
sina.nassiri
▴ 130
6
votes
6
replies
2.8k
views
EGSEA error during report generation: "only 0's may be mixed with negative subscripts"
EGSEA
updated 3.5 years ago by
Martin
• 0 • written 4.8 years ago by
pgugger
▴ 70
0
votes
5
replies
2.6k
views
EGSEA generateReport() error "no adj nodes"
EGSEA
EGSEA123
updated 6.4 years ago by
Monther Alhamdoosh
▴ 40 • written 6.4 years ago by
Jenny Drnevich
★ 2.0k
0
votes
1
reply
2.2k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger
dgelist
NA
egsea
updated 6.2 years ago by
Gordon Smyth
50k • written 6.2 years ago by
belmore
• 0
0
votes
3
replies
1.9k
views
Problem in kegga() and others getting data from KEGG after switch from http to https
limma
KEGGREST
EGSEA
updated 22 months ago by
shepherl
3.8k • written 22 months ago by
Jenny Drnevich
★ 2.0k
0
votes
4
replies
1.9k
views
EGSEA: how does the program generate the value for the up or down regulation of gene sets or pathways
pathways
gsea
egsea
gage
updated 7.6 years ago by
Monther Alhamdoosh
▴ 40 • written 7.6 years ago by
yingchen
• 0
2
votes
7
replies
1.8k
views
EGSEA - failing to write report
EGSEA
write
updated 7.2 years ago by
Monther Alhamdoosh
▴ 40 • written 7.2 years ago by
mforde84
▴ 20
2
votes
3
replies
1.6k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
7.3 years ago • updated 7.2 years ago
Pekka Kohonen
▴ 190
0
votes
2
replies
1.5k
views
Ensemble EGSEA (EGSEA): base GSA method failures
egsea
7.0 years ago
irizarnaunk
• 0
0
votes
2
replies
1.3k
views
How an index is built for each gene set collections using buildCustomIdx() indexing function of EGSEA package?
EGSEA
edgeR
biomaRt
limma
RNA-seq
4.7 years ago
fgol
▴ 10
1
vote
1
reply
1.1k
views
EGSEA : unable to plot heatmaps.
EGSEA
R bioconductor
6.6 years ago
RV
• 0
1
vote
0
replies
992
views
EGSEA install licensed KEGG data
EGSEA
KEGG
EGSEAdata
6.2 years ago
john.thompson
▴ 10
0
votes
0
replies
843
views
Contrast matrix for a continuous covariate - for EGSEA algorithm
design and contrast matrix
egsea
6.2 years ago
Stefano Mangiola
▴ 10
0
votes
1
reply
743
views
EGSEA::egsea - Parallelization issue and "Error in array(col.rgb[, i], dim(node.rgb)[3:1]) : negative length vectors are not allowed"
egsea
EGSEA123
12 months ago
neilzhao
▴ 30
1
vote
0
replies
714
views
EGSEA - clarification of values in the Stats Table
egsea
limma
4.6 years ago
rocanja
▴ 60
0
votes
1
reply
369
views
Is it possible to use pre-ranked list in EGSEA?
EGSEA
EGSEAdata
EGSEA123
DifferentialExpression
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
Tiago
• 0
0
votes
1
reply
266
views
EGSEA with Affymetrix data
EGSEA
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
cverschoor
• 0
17 results • Page
1 of 1
Recent ...
Replies
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…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
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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Gordon Smyth
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