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Showing :
goseq
•
reset
0
votes
2
replies
141
views
goseq: Wallenius Vs Fisher's Noncentral Hypergeometric Distribution
goseq
26 days ago • updated 25 days ago
Steve Pederson
▴ 170
1
vote
2
replies
156
views
Pathway analysis of RNAseq data using goseq package
Pathways
goseq
RNASeqData
10 weeks ago • updated 8 weeks ago
m.glymenaki
• 0
0
votes
0
replies
96
views
Gage pathway analysis of RNAseq graphical representation as dot plot
gage
plot
RNASeq
goseq
updated 10 weeks ago by
Michael Love
37k • written 10 weeks ago by
m.glymenaki
• 0
1
vote
10
replies
971
views
How to run Goseq for list of ensembl gene IDs
goseq
14 months ago • updated 13 months ago
Lucky
• 0
1
vote
4
replies
506
views
goseq package loading issues
DESeq2
goseq
15 months ago
avinashi
• 0
3
votes
9
replies
698
views
Warning message when performing Gene Ontology analysis with goseq using hg38
goseq
updated 15 months ago by
James W. MacDonald
59k • written 15 months ago by
Nikolay Ivanov
• 0
2
votes
3
replies
565
views
Gene Ontology Analysis of DE Genes
clusterProfiler
AnnotationDbi
OrgDb
goseq
updated 16 months ago by
James W. MacDonald
59k • written 16 months ago by
vanbelj
▴ 10
2
votes
2
replies
411
views
Pathway analysis and GO terms analysis with goseq
KEGG
Pathways
GO
goseq
updated 17 months ago by
James W. MacDonald
59k • written 17 months ago by
ojong
• 0
0
votes
1
reply
361
views
non-native GO annotation cannot be successfully introduced into Goseq
goseq
rnaseq
r
updated 19 months ago by
James W. MacDonald
59k • written 19 months ago by
citronxu
• 0
1
vote
2
replies
332
views
GOSeq analysis in rice
goseq
23 months ago • updated 21 months ago
nabiyogesh
▴ 10
0
votes
2
replies
247
views
Goseq_analysis related help
goseq
23 months ago • updated 22 months ago
kumararya563
• 0
0
votes
0
replies
196
views
go seq related help, where I need to do mapping between go term and the protein -id
goseq
23 months ago • updated 22 months ago
kumararya563
• 0
2
votes
2
replies
360
views
Goseq analysis related help.
annotation
goseq
updated 23 months ago by
Steve Lianoglou
13k • written 23 months ago by
kumararya563
• 0
0
votes
0
replies
245
views
How to identify differentially expressed genes from Reactome pathways enriched according to GOseq?
goseq
go
rna-seq
2.1 years ago
hasse.bossenbroek
• 0
4
votes
5
replies
987
views
Downgrading R to 3.6.0 version (GOseq problem)
goseq
installation
2.4 years ago
gdalsky
▴ 40
0
votes
1
reply
926
views
GO enrichment analysis graphs after goseq: any easy solutions?
go enrichment
gene ontology
goseq
go
2.7 years ago
Raito92
▴ 60
2
votes
6
replies
471
views
Can't install GOSEQ (dependency problem) on CentOS 7!
goseq
r package
r
updated 2.7 years ago by
Mike Smith
★ 5.5k • written 2.7 years ago by
Raito92
▴ 60
1
vote
1
reply
565
views
GOseq analysis with only upregulated or downregulated genes
goseq
updated 3.1 years ago by
Nadia Davidson
▴ 310 • written 3.1 years ago by
charles.foster
▴ 110
2
votes
2
replies
506
views
Using GOseq for custom gene set enrichment test
goseq
updated 3.3 years ago by
Gordon Smyth
45k • written 3.3 years ago by
kubovcij
• 0
0
votes
2
replies
966
views
How to access gene IDs associated with GO terms in GOSeq
GOseq
ensemblid
GO
updated 3.5 years ago by
James W. MacDonald
59k • written 3.5 years ago by
mico
• 0
4
votes
10
replies
2.1k
views
Question: GoSeq: opposite pwf plot for up- and downregulated genes
goseq
6.6 years ago • updated 3.5 years ago
Jakub
▴ 50
1
vote
3
replies
1.0k
views
goseq: Formatting category list for use with goseq
goseq
category test
updated 3.7 years ago by
James W. MacDonald
59k • written 3.7 years ago by
Mthabisi Moyo
▴ 30
0
votes
0
replies
457
views
how to: enrichment (over representation) analysis of GWAS/QTL data distributed over a genome with GOSEQ
goseq
enrichment
GWAS
3.8 years ago
zhu
• 0
0
votes
1
reply
647
views
GOseq output but strange warning message!
GOseq
GO
pwf
goseq
3.8 years ago
TB18
• 0
1
vote
1
reply
543
views
Goseq output with too many GO terms per category
go
goseq
goterm
category
updated 3.8 years ago by
Gordon Smyth
45k • written 3.8 years ago by
Juan
• 0
3
votes
2
replies
544
views
numInCat in goseq inconsistent with value obtained from org.Hs.eg.db
goseq
updated 3.8 years ago by
James W. MacDonald
59k • written 3.8 years ago by
siajunren
• 0
1
vote
9
replies
1.1k
views
Using goseq with unsupported organism
goseq
updated 3.8 years ago by
James W. MacDonald
59k • written 3.9 years ago by
Mehdi
• 0
0
votes
0
replies
476
views
GOseq No Underrepresented Categories
goseq
go enrichment
3.9 years ago
mart1139
• 0
8
votes
10
replies
787
views
Genes listed in GO categories
goseq
biomart
updated 3.9 years ago by
Gordon Smyth
45k • written 4.0 years ago by
frezende
• 0
0
votes
2
replies
510
views
goseq with hypergeometric method
goseq
updated 4.0 years ago by
Gordon Smyth
45k • written 4.0 years ago by
sharvari gujja
▴ 30
0
votes
0
replies
838
views
I finally solved my problem with installing "org.Hs.eg.db"!
goseq
org.hs.eg.db
4.1 years ago
nancyjwahl7
• 0
2
votes
6
replies
1.1k
views
Can Tximport average transcript length be used for GOSeq?
deseq2
tximport
goseq
4.2 years ago
casey.rimland
▴ 140
0
votes
6
replies
817
views
How to link methylation code from UCSC (hg19-cg07790169) to ENSEMBL genome code (goseq procedure)
goseq
methylation
ensembl
ucsc
limma
4.3 years ago • updated 4.2 years ago
dusan.petrovic
• 0
0
votes
2
replies
2.4k
views
DESeq2 followed by goseq GO-analysis: Extracting DE genes of enriched GO category
deseq2
goseq
rnaseq
go enrichment
differential gene expression
updated 4.3 years ago by
Michael Love
37k • written 4.3 years ago by
josef.oeckl
• 0
0
votes
3
replies
661
views
What is the impact of using GOSeq to voom-adjusted RNA-seq Expressions ?
limma
limma-voom
goseq
updated 4.3 years ago by
Gordon Smyth
45k • written 4.3 years ago by
joelrosa
• 0
0
votes
1
reply
2.1k
views
installation of package 'goseq' had non-zero exit status
goseq
installation
updated 4.5 years ago by
Martin Morgan
25k • written 4.5 years ago by
philipp.voss
• 0
0
votes
1
reply
1.1k
views
PANTHER.db- external pointer error
goseq
pantherdb
pathway analysis
gene ontology
updated 4.5 years ago by
James W. MacDonald
59k • written 4.5 years ago by
krc3004
▴ 10
1
vote
2
replies
2.1k
views
GOseq: Determining ENSG IDs Associated with Genes Summarized by `numDEInCat` for Each Ontology Term
goseq
gene ontology
updated 4.6 years ago by
James W. MacDonald
59k • written 4.6 years ago by
JMallory
• 0
0
votes
1
reply
748
views
Error: subscript out of bounds when using ucscGenomes() and supportedGenomes() functions in goseq and rtracklayer packages respctively
goseq
rtracklayer
4.6 years ago
mgdrnl
• 0
2
votes
3
replies
923
views
GOseq error on running nullp
goseq
GO term
updated 4.6 years ago by
Gordon Smyth
45k • written 4.6 years ago by
pereyra.s
• 0
0
votes
1
reply
1.5k
views
GO.db won't install for using goseq package
GO.db
goseq
package installation
error
updated 4.7 years ago by
Martin Morgan
25k • written 4.7 years ago by
veerle
• 0
0
votes
2
replies
980
views
bias.data vector must have the same length as DEgenes vector!
edger
goseq
updated 4.7 years ago by
Aaron Lun
★ 27k • written 4.7 years ago by
mictadlo
• 0
0
votes
0
replies
687
views
gene length file for GOseq
goseq
4.7 years ago
mictadlo
• 0
2
votes
2
replies
841
views
Error in normSplitFactor(f, x)
GenomicRanges
rtracklayer
goseq
updated 4.7 years ago by
Michael Lawrence
11k • written 4.7 years ago by
mictadlo
• 0
0
votes
3
replies
923
views
goseq after edgeR
edger
goseq
updated 4.7 years ago by
Aaron Lun
★ 27k • written 4.7 years ago by
mictadlo
• 0
0
votes
2
replies
1.1k
views
GOseq: Correct for gene length or read count?
goseq
dexseq
4.8 years ago • updated 4.7 years ago
i.sudbery
▴ 30
1
vote
1
reply
2.0k
views
goseq: In pcls(G) : initial point very close to some inequality constraints
goseq
warning message
pwf
mgcv
updated 4.7 years ago by
Nadia Davidson
▴ 310 • written 4.8 years ago by
heikki.sarin
▴ 10
1
vote
1
reply
850
views
PANTHER.db function not found
pantherdb
goseq
biomart
updated 4.8 years ago by
Mike Smith
★ 5.5k • written 4.8 years ago by
krc3004
▴ 10
3
votes
5
replies
1.0k
views
Does DEseq2 analysis make GOseq redundant?
deseq2
goseq
gene ontology
differential gene expression
4.8 years ago
david.rinker
▴ 10
0
votes
3
replies
1.6k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq
gene ontology
biomart
annotate
category
updated 4.9 years ago by
b.nota
▴ 360 • written 4.9 years ago by
krc3004
▴ 10
50 results • Page
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Comment: CPM after RUVseq
by
James W. MacDonald
59k
Also, you might be confused about something. CPM is counts/million counts, which *uses library size to scale normalize* and logCPM is just…
Comment: CPM after RUVseq
by
James W. MacDonald
59k
You shouldn't use CPM or logCPM for any of the steps! To use `RUVr` you need to fit a preliminary model using `edgeR`, which takes counts a…
Comment: CPM after RUVseq
by
Jess
• 0
Thank you James! It hadn't occurred to me to input CPM rather than logCPM which is why my df$NormalizedCounts didn't exceed 17ish in valu…
Answer: RPX PXDataset error
by
Laurent Gatto
1.5k
- From the URL in the error, it looks like you have the latest (or a recent) `rpx` version. It is generally recommended to add the output o…
Answer: Package name already exists due to previous issue
by
shepherl
3.1k
This has been resolved. There needed to be a manual intervention by the core team to remove the old issue from the issue tracker database.…
Votes
Answer: CPM after RUVseq
Comment: Merging two plated in R
Answer: Merging two plated in R
Answer: Merging two plated in R
A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
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