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goseq
•
reset
0
votes
0
replies
1.7k
views
gene length file for GOseq
goseq
8.2 years ago
mictadlo
▴ 10
2
votes
2
replies
1.9k
views
Error in normSplitFactor(f, x)
GenomicRanges
rtracklayer
goseq
updated 8.2 years ago by
Michael Lawrence
★ 11k • written 8.2 years ago by
mictadlo
▴ 10
0
votes
3
replies
1.9k
views
goseq after edgeR
edger
goseq
updated 8.2 years ago by
Aaron Lun
★ 29k • written 8.2 years ago by
mictadlo
▴ 10
0
votes
2
replies
2.0k
views
GOseq: Correct for gene length or read count?
goseq
dexseq
8.2 years ago
i.sudbery
▴ 40
1
vote
1
reply
3.4k
views
goseq: In pcls(G) : initial point very close to some inequality constraints
goseq
warning message
pwf
mgcv
updated 8.2 years ago by
Nadia Davidson
▴ 320 • written 8.2 years ago by
heikki.sarin
▴ 10
1
vote
1
reply
1.7k
views
PANTHER.db function not found
pantherdb
goseq
biomart
updated 8.3 years ago by
Mike Smith
★ 6.6k • written 8.3 years ago by
krc3004
▴ 10
3
votes
5
replies
2.2k
views
Does DEseq2 analysis make GOseq redundant?
deseq2
goseq
gene ontology
differential gene expression
8.3 years ago
david.rinker
▴ 10
0
votes
3
replies
2.8k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq
gene ontology
biomart
annotate
category
updated 8.3 years ago by
b.nota
▴ 370 • written 8.4 years ago by
krc3004
▴ 10
0
votes
1
reply
1.3k
views
installing getgo package
rnaseq
goseq
package installation
updated 8.5 years ago by
James W. MacDonald
68k • written 8.5 years ago by
sr17
• 0
2
votes
5
replies
2.5k
views
GOseq: count bias correction variations?
Coverage
goseq
updated 8.6 years ago by
Gordon Smyth
53k • written 11.3 years ago by
Christopher Conley
▴ 40
1
vote
6
replies
2.2k
views
goseq Error: could not find function "supportedOrganisms"
goseq
updated 8.6 years ago by
edmund.wright
• 0 • written 8.7 years ago by
colaneri
▴ 30
2
votes
2
replies
1.9k
views
goseq ERROR: SupportedOrganisms() subscript out of bounds
goseq
8.7 years ago
jesykamelendez
▴ 20
0
votes
5
replies
1.9k
views
goseq - supportedOrganisms error
go
goseq
updated 8.7 years ago by
Gordon Smyth
53k • written 8.7 years ago by
starbug16
• 0
1
vote
6
replies
2.9k
views
GoSeq SupportedGenomes error
goseq
unsupported organisms
supportedgenomes
supportedorganisms
error
updated 8.7 years ago by
Gordon Smyth
53k • written 8.7 years ago by
tootiki
• 0
2
votes
8
replies
3.3k
views
GOseq package: Which genes are included in the "numDEInCat"?
GOseq
KEGG
8.8 years ago
Xavier
▴ 10
2
votes
3
replies
3.2k
views
Goseq analysis with Biocarta, Reactome, and NCI pathways?
goseq
graphite
10.7 years ago • updated 8.9 years ago
b.nota
▴ 370
2
votes
1
reply
2.6k
views
Problems with GOseq
goseq
updated 9.1 years ago by
Nadia Davidson
▴ 320 • written 9.1 years ago by
webquelzinhablue
▴ 10
0
votes
2
replies
1.4k
views
how to incorporate count bias in Goseq
goseq
edgeR
updated 9.2 years ago by
anthony.hawkins
▴ 10 • written 9.2 years ago by
assaf www
▴ 140
0
votes
2
replies
1.9k
views
Extract all data from goseq (gene list with goterms)
r
goseq
go
updated 9.3 years ago by
Nadia Davidson
▴ 320 • written 9.3 years ago by
tobal.92
• 0
3
votes
1
reply
2.0k
views
goseq pwf length bias plot: interpreting plot
goseq
updated 9.3 years ago by
Gordon Smyth
53k • written 9.3 years ago by
Darya Vanichkina
▴ 130
3
votes
4
replies
2.2k
views
Trying to account for gene length in topGO analysis
topgo
goseq
deseq2
updated 9.4 years ago by
Bernd Klaus
▴ 610 • written 9.4 years ago by
Ben Mansfeld
• 0
1
vote
4
replies
2.2k
views
GOSeq: analysis of unsupported genome after HTseq and DEseq2 - building gene lengths, comparing contrasts and understanding results.
deseq2
goseq
htseqcounts
rnaseq
plant
updated 9.4 years ago by
Gordon Smyth
53k • written 9.4 years ago by
Ben Mansfeld
• 0
1
vote
3
replies
1.8k
views
How to resolve length bias and get GO/KEGG pathway for "non-standard" species in limma or goseq ?
rna-seq
limma
goseq
updated 9.5 years ago by
Nadia Davidson
▴ 320 • written 9.5 years ago by
CandiceChuDVM
▴ 40
0
votes
0
replies
2.0k
views
GOseq tutorial for not supported organisms: am I doing it correctly?
deseq2
goseq
biomart
r
rnaseq
9.5 years ago
CandiceChuDVM
▴ 40
2
votes
3
replies
1.7k
views
Can we use Entrez IDs for GOSeq?
goseq
entrez gene identifiers
updated 9.5 years ago by
James W. MacDonald
68k • written 9.5 years ago by
Mehmet Ilyas Cosacak
• 0
4
votes
6
replies
7.1k
views
goseq: not able to limit by GO categories when using wallenius approximation for over-representation test
goseq
updated 9.6 years ago by
Nadia Davidson
▴ 320 • written 9.6 years ago by
mrodrigues.fernanda
▴ 10
0
votes
5
replies
3.0k
views
How to get list of genes that are DE from the goseq analysis results
limma
goseq
mget
edgeR
updated 9.6 years ago by
Gordon Smyth
53k • written 9.6 years ago by
darshinimamindla
▴ 10
2
votes
4
replies
2.8k
views
goseq pwf length bias plot: help interpreting plot
goseq
updated 9.6 years ago by
Nadia Davidson
▴ 320 • written 9.6 years ago by
mrodrigues.fernanda
▴ 10
2
votes
2
replies
1.5k
views
goseq package: Is the package in sync with the most current Ensembl release?
goseq
ensembl
updated 9.6 years ago by
Johannes Rainer
★ 2.1k • written 9.6 years ago by
mrodrigues.fernanda
▴ 10
0
votes
4
replies
5.6k
views
goseq analysis - extracting list of my genes which are DE in the enriched GO category
GO
Category
goseq
GO
Category
goseq
updated 9.6 years ago by
darshinimamindla
▴ 10 • written 14.2 years ago by
Helen Wright
▴ 10
1
vote
2
replies
1.2k
views
goseq package: cannot find function supportedOrganisms()
goseq
updated 9.6 years ago by
Nadia Davidson
▴ 320 • written 9.6 years ago by
mrodrigues.fernanda
▴ 10
0
votes
4
replies
2.2k
views
danRer10 is missing in geneLenDataBase
genelendatabase
goseq
updated 9.7 years ago by
Nadia Davidson
▴ 320 • written 9.7 years ago by
Mehmet Ilyas Cosacak
• 0
0
votes
1
reply
1.4k
views
Error using goseq function in bioconductor pkg goseq
goseq
updated 9.7 years ago by
Gordon Smyth
53k • written 9.7 years ago by
jdavison
▴ 10
1
vote
2
replies
2.9k
views
goseq: Can't find mm10/geneSymbol length data in genLenDataBase...
goseq
9.8 years ago
Bohdan Khomtchouk
▴ 10
3
votes
10
replies
3.3k
views
How to use GOseq without length bias
goseq
updated 9.8 years ago by
Steve Lianoglou
★ 13k • written 9.8 years ago by
b.nota
▴ 370
2
votes
6
replies
2.1k
views
Print to txt file in specific way
goseq
sink
cat
print
updated 9.8 years ago by
Mike Smith
★ 6.6k • written 9.8 years ago by
b.nota
▴ 370
5
votes
7
replies
6.0k
views
Using goseq on non-model organism - how to define genome?
goseq
go
genesetenrichment
updated 9.9 years ago by
Gordon Smyth
53k • written 9.9 years ago by
Jon Bråte
▴ 270
0
votes
1
reply
1.5k
views
accounting for gene length with SeqGSEA
goseq
SeqGSEA
goseq
SeqGSEA
updated 10.0 years ago by
Xi Wang
• 0 • written 12.4 years ago by
Julie Leonard
▴ 110
13
votes
2
replies
5.4k
views
Best method/package for Gene Set Enrichment Analysis in microarrays?
GSEA
goseq
topgo
gega
gostats
updated 10.0 years ago by
Robert Castelo
★ 3.4k • written 10.0 years ago by
jacorvar
▴ 40
3
votes
7
replies
5.2k
views
goseq code after DESeq2 -NO IDEA!
goseq
DESEQ2
RSTUDIO
CODE
updated 10.0 years ago by
Steve Lianoglou
★ 13k • written 10.0 years ago by
amyfm
▴ 10
0
votes
4
replies
3.7k
views
Impossible to use goseq package - problem with geneLenDataBase
goseq
geneLenDataBase
bioclite
rstudio
updated 10.0 years ago by
Martin Morgan
25k • written 10.0 years ago by
amyfm
▴ 10
0
votes
2
replies
1.2k
views
Weird result with GOseq
goseq
updated 10.2 years ago by
Gordon Smyth
53k • written 10.2 years ago by
dlsoltero
• 0
0
votes
1
reply
1.9k
views
goseq: probability weighting function returns NA for bias and weighting info. for some genes (mm10); why?
goseq
pwf
updated 10.2 years ago by
Nadia Davidson
▴ 320 • written 10.2 years ago by
mjnolte
• 0
2
votes
2
replies
2.5k
views
Goseq supported organism (felcat5) has an error when testing
goseq
genesetenrichment
annotation
updated 10.2 years ago by
Nadia Davidson
▴ 320 • written 10.2 years ago by
xyliu00
▴ 20
0
votes
0
replies
2.4k
views
How to use REVIGO to remove redundant GO term
goseq
revigo
10.2 years ago
jackipchiho
▴ 10
0
votes
1
reply
1.8k
views
Goseq with small numbers of genes: minimum number?
goseq
10.2 years ago
matt.arno
• 0
0
votes
1
reply
1.7k
views
Failed attempts to download or load GeneLenDataBase package
goseq
genelendatabase
10.2 years ago
FeiYian Yoong
▴ 30
2
votes
5
replies
2.9k
views
goseq error--"in names(tmp) = rep(names(map)"
goseq
updated 10.3 years ago by
Nadia Davidson
▴ 320 • written 10.3 years ago by
xdzperfect
• 0
2
votes
4
replies
3.9k
views
About GOSeq GO and KEGG enrichment analysis
goseq
10.3 years ago
jackipchiho
▴ 10
0
votes
2
replies
1.5k
views
Conditional test for goseq?
goseq
gostats
updated 10.3 years ago by
Gordon Smyth
53k • written 10.3 years ago by
Johannes Rainer
★ 2.1k
162 results • Page
2 of 4
Recent ...
Replies
Answer: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
This should now be resolved
Answer: Question about collapsing ASVs by genus level during DESeq2 analysis
by
Michael Love
43k
I'll just note that microbiome stats folks tend to use other tools than DESeq2. > several ASVs belong to the same genus but are not iden…
Answer: Integration: Paired-end vs healthy single-end from a different source
by
James W. MacDonald
68k
If by reprocess you mean generate libraries and re-sequence, then that's something you could do. Otherwise the biological and technical dif…
Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
we can investigate this issue. thank you for bringing it to our attention
Votes
Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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