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EGSEA
•
reset
3
votes
5
replies
823
views
Help with running egsea()
EGSEA
10 months ago
Chris
▴ 20
0
votes
1
reply
530
views
EGSEA with Affymetrix data
EGSEA
updated 16 months ago by
James W. MacDonald
68k • written 16 months ago by
cverschoor
• 0
0
votes
1
reply
677
views
Is it possible to use pre-ranked list in EGSEA?
EGSEA
EGSEAdata
EGSEA123
DifferentialExpression
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
Tiago
• 0
0
votes
1
reply
1.1k
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
23 months ago
neilzhao
▴ 30
0
votes
3
replies
2.7k
views
Problem in kegga() and others getting data from KEGG after switch from http to https
limma
KEGGREST
EGSEA
updated 2.7 years ago by
shepherl
4.1k • written 2.7 years ago by
Jenny Drnevich
★ 2.0k
6
votes
6
replies
3.5k
views
EGSEA error during report generation: "only 0's may be mixed with negative subscripts"
EGSEA
updated 4.4 years ago by
Martin
• 0 • written 5.7 years ago by
pgugger
▴ 70
1
vote
0
replies
913
views
EGSEA - clarification of values in the Stats Table
egsea
limma
5.5 years ago
rocanja
▴ 60
0
votes
2
replies
1.6k
views
How an index is built for each gene set collections using buildCustomIdx() indexing function of EGSEA package?
EGSEA
edgeR
biomaRt
limma
RNA-seq
5.6 years ago
fgol
▴ 10
9
votes
7
replies
21k
views
Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea
gsva
piano
egsea
updated 15 months ago by
amin8w
▴ 10 • written 7.6 years ago by
sina.nassiri
▴ 130
0
votes
1
reply
2.6k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger
dgelist
NA
egsea
updated 7.1 years ago by
Gordon Smyth
52k • written 7.1 years ago by
belmore
• 0
1
vote
0
replies
1.3k
views
EGSEA install licensed KEGG data
EGSEA
KEGG
EGSEAdata
7.1 years ago
john.thompson
▴ 10
0
votes
0
replies
1.0k
views
Contrast matrix for a continuous covariate - for EGSEA algorithm
design and contrast matrix
egsea
7.1 years ago
Stefano Mangiola
▴ 40
0
votes
5
replies
3.0k
views
EGSEA generateReport() error "no adj nodes"
EGSEA
EGSEA123
updated 7.3 years ago by
Monther Alhamdoosh
▴ 40 • written 7.3 years ago by
Jenny Drnevich
★ 2.0k
1
vote
1
reply
1.4k
views
EGSEA : unable to plot heatmaps.
EGSEA
R bioconductor
7.5 years ago
RV
• 0
0
votes
2
replies
1.8k
views
Ensemble EGSEA (EGSEA): base GSA method failures
egsea
7.9 years ago
irizarnaunk
• 0
2
votes
7
replies
2.2k
views
EGSEA - failing to write report
EGSEA
write
updated 8.1 years ago by
Monther Alhamdoosh
▴ 40 • written 8.1 years ago by
mforde84
▴ 20
2
votes
4
replies
2.0k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
updated 10 months ago by
Chris
▴ 20 • written 8.2 years ago by
Pekka Kohonen
▴ 190
0
votes
4
replies
2.3k
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 8.5 years ago by
Monther Alhamdoosh
▴ 40 • written 8.5 years ago by
yingchen
• 0
18 results • Page
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Replies
Answer: affy::rma results doesn't match with ncbi website
by
ATpoint
★ 4.7k
Exact OMCIS reproduction down to the values without code and software version is borderline impossible. Either use the values as provided o…
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
by
James W. MacDonald
68k
You've got it backwards. It should be ``` adult_res_df$symbol <- mapIds(org.Rn.eg.db, keys = rownames(adult_res_df), column = "ENSEMBL"…
Comment: DESeq2 swap ensembl gene id rownames with gene symbol column
by
Erika
• 0
Alternatively, you could have added a column with the common gene names. Assuming your dataframe `df` was created using `DESeq()`, somethin…
Answer: Clarification on GOALL / GO2ALLORFs mapping
by
James W. MacDonald
68k
It appears that 'negative regulation of glycogen biosynthesis' has an 'is a' relationship with 'glycogen biosynthetic process' https://www.…
Comment: Can't post a question?
by
DavideSant
• 0
Thank you, this was super useful!
Votes
Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf
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Gordon Smyth
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