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Showing :
GOseq
•
reset
13
votes
2
replies
4.6k
views
Best method/package for Gene Set Enrichment Analysis in microarrays?
GSEA
goseq
topgo
gega
gostats
updated 8.5 years ago by
Robert Castelo
★ 3.3k • written 8.5 years ago by
jacorvar
▴ 40
8
votes
10
replies
1.6k
views
Genes listed in GO categories
goseq
biomart
updated 5.9 years ago by
Gordon Smyth
50k • written 6.0 years ago by
frezende
• 0
5
votes
7
replies
4.9k
views
Using goseq on non-model organism - how to define genome?
goseq
go
genesetenrichment
updated 8.4 years ago by
Gordon Smyth
50k • written 8.4 years ago by
Jon Bråte
▴ 250
5
votes
3
replies
2.5k
views
GOSEQ: could not find any categories for many genes
goseq
mm9
9.1 years ago
Vivek.b
▴ 100
5
votes
2
replies
1.4k
views
GoSeq: Wallenius 264 overrepresented sampling 0?
goseq
updated 9.0 years ago by
Gordon Smyth
50k • written 9.0 years ago by
idomtamir
▴ 10
4
votes
4
replies
7.8k
views
Packages for GO and KEGG analysis on RNAseq data
GO
gage
goseq
KEGG
updated 9.6 years ago by
Gordon Smyth
50k • written 9.7 years ago by
Merienne Nicolas
▴ 120
4
votes
6
replies
1.9k
views
goseq: not able to limit by GO categories when using wallenius approximation for over-representation test
goseq
updated 8.1 years ago by
Nadia Davidson
▴ 310 • written 8.1 years ago by
mrodrigues.fernanda
▴ 10
4
votes
5
replies
1.8k
views
Downgrading R to 3.6.0 version (GOseq problem)
goseq
installation
4.4 years ago
gdalsky
▴ 40
4
votes
10
replies
3.0k
views
Question: GoSeq: opposite pwf plot for up- and downregulated genes
goseq
8.6 years ago • updated 5.5 years ago
Jakub
▴ 50
3
votes
9
replies
1.9k
views
Warning message when performing Gene Ontology analysis with goseq using hg38
goseq
updated 3.2 years ago by
James W. MacDonald
66k • written 3.3 years ago by
Nikolay Ivanov
• 0
3
votes
4
replies
1.7k
views
Trying to account for gene length in topGO analysis
topgo
goseq
deseq2
updated 7.9 years ago by
Bernd Klaus
▴ 610 • written 7.9 years ago by
Ben Mansfeld
• 0
3
votes
5
replies
1.7k
views
Does DEseq2 analysis make GOseq redundant?
deseq2
goseq
gene ontology
differential gene expression
6.8 years ago
david.rinker
▴ 10
3
votes
10
replies
2.5k
views
How to use GOseq without length bias
goseq
updated 8.3 years ago by
Steve Lianoglou
★ 13k • written 8.3 years ago by
b.nota
▴ 360
3
votes
2
replies
1.1k
views
Goseq analysis related help.
annotation
goseq
updated 3.9 years ago by
Steve Lianoglou
★ 13k • written 3.9 years ago by
kumararya563
• 0
3
votes
2
replies
1.1k
views
numInCat in goseq inconsistent with value obtained from org.Hs.eg.db
goseq
updated 5.8 years ago by
James W. MacDonald
66k • written 5.8 years ago by
siajunren
• 0
3
votes
3
replies
2.0k
views
Goseq and yeast
goseq
yeast
9.3 years ago
Marek Gierlinski
▴ 30
3
votes
7
replies
4.6k
views
goseq code after DESeq2 -NO IDEA!
goseq
DESEQ2
RSTUDIO
CODE
updated 8.6 years ago by
Steve Lianoglou
★ 13k • written 8.6 years ago by
amyfm
▴ 10
3
votes
1
reply
1.7k
views
goseq pwf length bias plot: interpreting plot
goseq
updated 7.9 years ago by
Gordon Smyth
50k • written 7.9 years ago by
Darya Vanichkina
▴ 120
2
votes
3
replies
1.8k
views
GOseq error on running nullp
goseq
GO term
updated 6.6 years ago by
Gordon Smyth
50k • written 6.6 years ago by
pereyra.s
• 0
2
votes
6
replies
2.0k
views
Can Tximport average transcript length be used for GOSeq?
deseq2
tximport
goseq
6.2 years ago
casey.rimland
▴ 150
2
votes
2
replies
1.4k
views
Error in normSplitFactor(f, x)
GenomicRanges
rtracklayer
goseq
updated 6.7 years ago by
Michael Lawrence
★ 11k • written 6.7 years ago by
mictadlo
▴ 10
2
votes
2
replies
1.7k
views
goseq ERROR: SupportedOrganisms() subscript out of bounds
goseq
7.2 years ago
jesykamelendez
▴ 20
2
votes
1
reply
2.2k
views
Problems with GOseq
goseq
updated 7.7 years ago by
Nadia Davidson
▴ 310 • written 7.7 years ago by
webquelzinhablue
▴ 10
2
votes
8
replies
2.5k
views
GOseq package: Which genes are included in the "numDEInCat"?
GOseq
KEGG
7.3 years ago
Xavier
▴ 10
2
votes
3
replies
1.3k
views
Can we use Entrez IDs for GOSeq?
goseq
entrez gene identifiers
updated 8.0 years ago by
James W. MacDonald
66k • written 8.0 years ago by
Mehmet Ilyas Cosacak
• 0
2
votes
5
replies
4.0k
views
gene set enrichment analysis of RNA-Seq data
Microarray
goseq
Microarray
goseq
updated 12.1 years ago by
Gordon Smyth
50k • written 12.1 years ago by
Julie Leonard
▴ 110
2
votes
2
replies
1.2k
views
goseq package: Is the package in sync with the most current Ensembl release?
goseq
ensembl
updated 8.1 years ago by
Johannes Rainer
★ 2.0k • written 8.1 years ago by
mrodrigues.fernanda
▴ 10
2
votes
2
replies
1.1k
views
Pathway analysis and GO terms analysis with goseq
KEGG
Pathways
GO
goseq
updated 3.5 years ago by
James W. MacDonald
66k • written 3.5 years ago by
ojong
• 0
2
votes
3
replies
1.7k
views
Gene Ontology Analysis of DE Genes
clusterProfiler
AnnotationDbi
OrgDb
goseq
updated 3.3 years ago by
James W. MacDonald
66k • written 3.3 years ago by
vanbelj
▴ 30
2
votes
4
replies
2.3k
views
goseq pwf length bias plot: help interpreting plot
goseq
updated 8.1 years ago by
Nadia Davidson
▴ 310 • written 8.1 years ago by
mrodrigues.fernanda
▴ 10
2
votes
6
replies
1.6k
views
Print to txt file in specific way
goseq
sink
cat
print
updated 8.3 years ago by
Mike Smith
★ 6.5k • written 8.3 years ago by
b.nota
▴ 360
2
votes
4
replies
3.1k
views
About GOSeq GO and KEGG enrichment analysis
goseq
8.8 years ago
jackipchiho
▴ 10
2
votes
2
replies
1.1k
views
Using GOseq for custom gene set enrichment test
goseq
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
kubovcij
• 0
2
votes
2
replies
2.9k
views
How to access gene IDs associated with GO terms in GOSeq
GOseq
ensemblid
GO
updated 5.5 years ago by
James W. MacDonald
66k • written 5.5 years ago by
mico
• 0
2
votes
6
replies
1.1k
views
Can't install GOSEQ (dependency problem) on CentOS 7!
goseq
r package
r
updated 4.7 years ago by
Mike Smith
★ 6.5k • written 4.7 years ago by
Raito92
▴ 60
2
votes
2
replies
2.0k
views
Goseq supported organism (felcat5) has an error when testing
goseq
genesetenrichment
annotation
updated 8.8 years ago by
Nadia Davidson
▴ 310 • written 8.8 years ago by
xyliu00
▴ 20
2
votes
5
replies
2.0k
views
GOseq: count bias correction variations?
Coverage
goseq
updated 7.1 years ago by
Gordon Smyth
50k • written 9.8 years ago by
Christopher Conley
▴ 40
2
votes
1
reply
1.2k
views
GoSeq: use ENSEMBLTRANS as input
goseq
ensembl
updated 9.0 years ago by
Nadia Davidson
▴ 310 • written 9.0 years ago by
idomtamir
▴ 10
2
votes
7
replies
3.5k
views
mm10 ENSEMBL not available for GOSEQ
goseq
RNAseq
mm10
9.0 years ago
Merienne Nicolas
▴ 120
2
votes
3
replies
2.6k
views
Goseq analysis with Biocarta, Reactome, and NCI pathways?
goseq
graphite
9.3 years ago • updated 7.5 years ago
b.nota
▴ 360
2
votes
5
replies
2.4k
views
goseq error--"in names(tmp) = rep(names(map)"
goseq
updated 8.8 years ago by
Nadia Davidson
▴ 310 • written 8.8 years ago by
xdzperfect
• 0
2
votes
3
replies
282
views
package goseq seems to be not available on the latest version of R
goseq
updated 15 days ago by
Gordon Smyth
50k • written 17 days ago by
Patrycja
▴ 20
1
vote
1
reply
3.0k
views
goseq/nullp with non-native identifiers
Annotation
GO
zebrafish
goseq
Annotation
GO
zebrafish
goseq
updated 11.7 years ago by
Alicia Oshlack
▴ 100 • written 11.7 years ago by
Ravi Karra
▴ 140
1
vote
2
replies
2.9k
views
GOseq: Determining ENSG IDs Associated with Genes Summarized by `numDEInCat` for Each Ontology Term
goseq
gene ontology
updated 6.6 years ago by
James W. MacDonald
66k • written 6.6 years ago by
JMallory
• 0
1
vote
1
reply
2.8k
views
goseq: In pcls(G) : initial point very close to some inequality constraints
goseq
warning message
pwf
mgcv
updated 6.7 years ago by
Nadia Davidson
▴ 310 • written 6.8 years ago by
heikki.sarin
▴ 10
1
vote
1
reply
1.3k
views
PANTHER.db function not found
pantherdb
goseq
biomart
updated 6.8 years ago by
Mike Smith
★ 6.5k • written 6.8 years ago by
krc3004
▴ 10
1
vote
6
replies
1.7k
views
goseq Error: could not find function "supportedOrganisms"
goseq
updated 7.2 years ago by
edmund.wright
• 0 • written 7.2 years ago by
colaneri
▴ 30
1
vote
1
reply
1.3k
views
Error GOseq
goseq
goseq
updated 13.2 years ago by
Matthew Young
▴ 40 • written 13.2 years ago by
Biase, Fernando
▴ 150
1
vote
6
replies
2.5k
views
GoSeq SupportedGenomes error
goseq
unsupported organisms
supportedgenomes
supportedorganisms
error
updated 7.2 years ago by
Gordon Smyth
50k • written 7.2 years ago by
tootiki
• 0
1
vote
2
replies
2.5k
views
goseq: Can't find mm10/geneSymbol length data in genLenDataBase...
goseq
8.3 years ago
Bohdan Khomtchouk
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: ChAMP installation issue
by
Tahirah
• 0
Hello. Could you please share how you managed to install ChAMP in R 4.4.0? I also have R 4.4.0 and Bioconductor 3.19 version and ChAMP fail…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
by
James W. MacDonald
66k
Yes, you can use `limma`.
Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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