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goseq
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News:
Gene Set Enrichment Analysis in Bioconductor course
GSEABase
GeneSetEnrichment
goseq
4 weeks ago • updated 23 days ago
info
▴ 10
5
votes
9
replies
2.2k
views
Inconsistent nullp and goseq enrichment results across operating systems
goseq
written 8 months ago by
Danielle
• 0
2
votes
3
replies
1.0k
views
package goseq seems to be not available on the latest version of R
goseq
updated 10 months ago by
Gordon Smyth
52k • written 10 months ago by
Patrycja
▴ 20
1
vote
2
replies
607
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq
Bioconductor
rtracklayer
12 months ago
thomas
• 0
1
vote
4
replies
931
views
goseq, warning and strange plot from nullp
goseq
13 months ago
boczniak767
▴ 740
0
votes
1
reply
874
views
Downstream analysis with Differentially Expressed Genes
DESeq2
GO
goseq
FunctionalAnnotation
updated 2.4 years ago by
Laia
▴ 10 • written 2.4 years ago by
acram
• 0
0
votes
5
replies
3.1k
views
GO enrichment with non-model organism, supplying GO mappings
clusterProfiler
goseq
topGO
DESeq2
updated 2.8 years ago by
James W. MacDonald
68k • written 2.8 years ago by
Lucía
▴ 30
0
votes
2
replies
1.2k
views
goseq: Wallenius Vs Fisher's Noncentral Hypergeometric Distribution
goseq
2.9 years ago
Steve Pederson
▴ 170
1
vote
2
replies
1.2k
views
Pathway analysis of RNAseq data using goseq package
Pathways
goseq
RNASeqData
3.0 years ago
m.glymenaki
• 0
0
votes
0
replies
1.0k
views
Gage pathway analysis of RNAseq graphical representation as dot plot
gage
plot
RNASeq
goseq
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
m.glymenaki
• 0
1
vote
10
replies
3.3k
views
How to run Goseq for list of ensembl gene IDs
goseq
4.0 years ago
Lucky
• 0
1
vote
4
replies
1.9k
views
goseq package loading issues
DESeq2
goseq
4.1 years ago
avinashi
• 0
3
votes
9
replies
2.5k
views
Warning message when performing Gene Ontology analysis with goseq using hg38
goseq
updated 4.1 years ago by
James W. MacDonald
68k • written 4.1 years ago by
Nikolay Ivanov
• 0
2
votes
3
replies
2.3k
views
Gene Ontology Analysis of DE Genes
clusterProfiler
AnnotationDbi
OrgDb
goseq
updated 4.1 years ago by
James W. MacDonald
68k • written 4.2 years ago by
vanbelj
▴ 30
2
votes
2
replies
1.5k
views
Pathway analysis and GO terms analysis with goseq
KEGG
Pathways
GO
goseq
updated 4.3 years ago by
James W. MacDonald
68k • written 4.3 years ago by
ojong
• 0
0
votes
1
reply
1.2k
views
non-native GO annotation cannot be successfully introduced into Goseq
goseq
rnaseq
r
updated 4.4 years ago by
James W. MacDonald
68k • written 4.4 years ago by
citronxu
• 0
1
vote
2
replies
1.2k
views
GOSeq analysis in rice
goseq
4.8 years ago • updated 4.6 years ago
Jitendra
▴ 10
0
votes
2
replies
924
views
Goseq_analysis related help
goseq
4.7 years ago
kumararya563
• 0
0
votes
0
replies
647
views
go seq related help, where I need to do mapping between go term and the protein -id
goseq
4.7 years ago
kumararya563
• 0
3
votes
2
replies
1.4k
views
Goseq analysis related help.
annotation
goseq
updated 4.8 years ago by
Steve Lianoglou
★ 13k • written 4.8 years ago by
kumararya563
• 0
0
votes
0
replies
1.1k
views
How to identify differentially expressed genes from Reactome pathways enriched according to GOseq?
goseq
go
rna-seq
5.0 years ago
hasse.bossenbroek
• 0
4
votes
5
replies
2.2k
views
Downgrading R to 3.6.0 version (GOseq problem)
goseq
installation
5.2 years ago
gdalsky
▴ 40
0
votes
1
reply
2.6k
views
GO enrichment analysis graphs after goseq: any easy solutions?
go enrichment
gene ontology
goseq
go
5.5 years ago
Raito92
▴ 60
2
votes
6
replies
1.5k
views
Can't install GOSEQ (dependency problem) on CentOS 7!
goseq
r package
r
updated 5.5 years ago by
Mike Smith
★ 6.6k • written 5.5 years ago by
Raito92
▴ 60
2
votes
1
reply
2.0k
views
GOseq analysis with only upregulated or downregulated genes
goseq
updated 5.9 years ago by
Nadia Davidson
▴ 320 • written 5.9 years ago by
charles.foster
▴ 170
2
votes
2
replies
1.4k
views
Using GOseq for custom gene set enrichment test
goseq
updated 6.1 years ago by
Gordon Smyth
52k • written 6.1 years ago by
kubovcij
• 0
2
votes
2
replies
3.6k
views
How to access gene IDs associated with GO terms in GOSeq
GOseq
ensemblid
GO
updated 6.4 years ago by
James W. MacDonald
68k • written 6.4 years ago by
mico
• 0
4
votes
10
replies
3.6k
views
Question: GoSeq: opposite pwf plot for up- and downregulated genes
goseq
9.4 years ago • updated 6.4 years ago
Jakub
▴ 50
1
vote
3
replies
2.2k
views
goseq: Formatting category list for use with goseq
goseq
category test
updated 6.5 years ago by
James W. MacDonald
68k • written 6.5 years ago by
Mthabisi Moyo
▴ 40
0
votes
0
replies
1.1k
views
how to: enrichment (over representation) analysis of GWAS/QTL data distributed over a genome with GOSEQ
goseq
enrichment
GWAS
6.6 years ago
zhu
• 0
0
votes
1
reply
1.4k
views
GOseq output but strange warning message!
GOseq
GO
pwf
goseq
6.6 years ago
TB18
• 0
1
vote
1
reply
1.5k
views
Goseq output with too many GO terms per category
go
goseq
goterm
category
updated 6.6 years ago by
Gordon Smyth
52k • written 6.6 years ago by
Juan
• 0
3
votes
2
replies
1.3k
views
numInCat in goseq inconsistent with value obtained from org.Hs.eg.db
goseq
updated 6.6 years ago by
James W. MacDonald
68k • written 6.6 years ago by
siajunren
• 0
1
vote
9
replies
2.7k
views
Using goseq with unsupported organism
goseq
updated 6.7 years ago by
James W. MacDonald
68k • written 6.7 years ago by
Mehdi
• 0
0
votes
0
replies
1.1k
views
GOseq No Underrepresented Categories
goseq
go enrichment
6.7 years ago
mart1139
• 0
8
votes
10
replies
2.1k
views
Genes listed in GO categories
goseq
biomart
updated 6.8 years ago by
Gordon Smyth
52k • written 6.8 years ago by
frezende
• 0
0
votes
2
replies
1.1k
views
goseq with hypergeometric method
goseq
updated 6.8 years ago by
Gordon Smyth
52k • written 6.8 years ago by
sharvari gujja
▴ 40
0
votes
0
replies
1.6k
views
I finally solved my problem with installing "org.Hs.eg.db"!
goseq
org.hs.eg.db
7.0 years ago
nancyjwahl7
• 0
2
votes
6
replies
2.4k
views
Can Tximport average transcript length be used for GOSeq?
deseq2
tximport
goseq
7.0 years ago
casey.rimland
▴ 170
0
votes
6
replies
1.9k
views
How to link methylation code from UCSC (hg19-cg07790169) to ENSEMBL genome code (goseq procedure)
goseq
methylation
ensembl
ucsc
limma
7.1 years ago
dusan.petrovic
• 0
0
votes
2
replies
4.1k
views
DESeq2 followed by goseq GO-analysis: Extracting DE genes of enriched GO category
deseq2
goseq
rnaseq
go enrichment
differential gene expression
updated 7.1 years ago by
Michael Love
43k • written 7.1 years ago by
josef.oeckl
• 0
0
votes
3
replies
1.5k
views
What is the impact of using GOSeq to voom-adjusted RNA-seq Expressions ?
limma
limma-voom
goseq
updated 7.1 years ago by
Gordon Smyth
52k • written 7.1 years ago by
joelrosa
• 0
0
votes
1
reply
2.9k
views
installation of package 'goseq' had non-zero exit status
goseq
installation
updated 7.3 years ago by
Martin Morgan
25k • written 7.3 years ago by
philipp.voss
• 0
0
votes
1
reply
2.0k
views
PANTHER.db- external pointer error
goseq
pantherdb
pathway analysis
gene ontology
updated 7.3 years ago by
James W. MacDonald
68k • written 7.3 years ago by
krc3004
▴ 10
1
vote
2
replies
3.3k
views
GOseq: Determining ENSG IDs Associated with Genes Summarized by `numDEInCat` for Each Ontology Term
goseq
gene ontology
updated 7.4 years ago by
James W. MacDonald
68k • written 7.4 years ago by
JMallory
• 0
0
votes
1
reply
1.4k
views
Error: subscript out of bounds when using ucscGenomes() and supportedGenomes() functions in goseq and rtracklayer packages respctively
goseq
rtracklayer
7.4 years ago
mgdrnl
• 0
2
votes
3
replies
2.1k
views
GOseq error on running nullp
goseq
GO term
updated 7.5 years ago by
Gordon Smyth
52k • written 7.5 years ago by
pereyra.s
• 0
0
votes
1
reply
2.2k
views
GO.db won't install for using goseq package
GO.db
goseq
package installation
error
updated 7.5 years ago by
Martin Morgan
25k • written 7.5 years ago by
veerle
• 0
0
votes
2
replies
1.9k
views
bias.data vector must have the same length as DEgenes vector!
edger
goseq
updated 7.5 years ago by
Aaron Lun
★ 28k • written 7.5 years ago by
mictadlo
▴ 10
0
votes
0
replies
1.5k
views
gene length file for GOseq
goseq
7.5 years ago
mictadlo
▴ 10
50 results • Page
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Comment: DiffBind custom normalization factor
by
Abbie
• 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
by
James W. MacDonald
68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore
by
Kent
• 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore
by
Michael Love
43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi
by
Michael Love
43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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