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Goseq output with too many GO terms per category
go
goseq
goterm
category
updated 5.7 years ago by
Gordon Smyth
50k • written 5.7 years ago by
Juan
• 0
0
votes
3
replies
2.2k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq
gene ontology
biomart
annotate
category
updated 6.8 years ago by
b.nota
▴ 360 • written 6.8 years ago by
krc3004
▴ 10
1
vote
0
replies
1.3k
views
enrichment analysis for gene pairs
go
gostats
category
gsea
8.5 years ago
Hector Corrada Bravo
▴ 60
0
votes
0
replies
1.3k
views
hyperGTest for MSigDB categories
category
gostats
msigdb
hypergeometric test
8.7 years ago
petyuk
▴ 70
0
votes
8
replies
2.1k
views
PFAM Enrichment in GOstats
PFAM
Category
GOstats
updated 9.0 years ago by
Guangchuang Yu
★ 1.2k • written 9.0 years ago by
Iain Gallagher
▴ 930
2
votes
2
replies
1.1k
views
rownames for categoryReshape
Category
updated 9.4 years ago by
Martin Morgan
25k • written 9.4 years ago by
alison.sara.waller
• 0
1
vote
0
replies
1.2k
views
how to fetch GO categories from Chinese hamster genome
GO
Category
goseq
9.6 years ago
upendra kumar devisetty
▴ 30
0
votes
1
reply
1.4k
views
GO enrichment
GO
Category
goseq
GO
Category
goseq
9.7 years ago
Guest User
★ 13k
0
votes
1
reply
1.6k
views
snpStats reference allele used in genetic associations?
SNP
Category
snpStats
SNP
Category
snpStats
updated 9.9 years ago by
Vincent J. Carey, Jr.
6.7k • written 9.9 years ago by
Guest User
★ 13k
0
votes
0
replies
1.8k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO
Category
sva
GO
Category
sva
10.1 years ago
Magda Price
▴ 60
0
votes
8
replies
4.8k
views
ComBat: 3 adjustment variables & continuous adjustment variables
GO
Category
sva
GO
Category
sva
updated 10.1 years ago by
Steve Lianoglou
★ 13k • written 10.1 years ago by
Guest User
★ 13k
0
votes
0
replies
2.0k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO
Category
sva
GO
Category
sva
10.2 years ago
W. Evan Johnson
▴ 850
0
votes
0
replies
1.7k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO
Category
sva
GO
Category
sva
10.2 years ago
Magda Price
▴ 60
0
votes
0
replies
1.7k
views
R pathview and mouse
Category
pathview
Category
pathview
10.3 years ago
Luo Weijun
★ 1.6k
0
votes
1
reply
1.9k
views
Analysis of Affymetrix Human Gene 2.0 ST arrays
Transcription
Annotation
Normalization
GO
hgu133plus2
affy
PROcess
Category
Transcription
updated 10.4 years ago by
Federico Lasa
▴ 80 • written 10.4 years ago by
María Maqueda González
▴ 20
0
votes
4
replies
3.6k
views
Analysis of Affymetrix Human Gene 2.0 ST arrays
Annotation
Normalization
hgu133plus2
affy
PROcess
Category
Annotation
Normalization
affy
updated 10.4 years ago by
James W. MacDonald
65k • written 10.4 years ago by
Guest User
★ 13k
0
votes
1
reply
1.0k
views
GSEABase error parsing msigdb_v4.0.xml
Category
Category
updated 10.5 years ago by
Martin Morgan
25k • written 10.5 years ago by
Milica Ng
▴ 10
0
votes
0
replies
1.3k
views
enrichment packages that accept t-stat (or related stat) as input
Microarray
limma
Category
CAMERA
GSVA
Microarray
limma
Category
CAMERA
GSVA
10.5 years ago
Gordon Smyth
50k
0
votes
0
replies
1.2k
views
enrichment packages that accept t-stat (or related stat) as input
Microarray
Proteomics
limma
Category
CAMERA
GSVA
Microarray
Proteomics
limma
Category
10.5 years ago
Pekka Kohonen
▴ 190
0
votes
1
reply
925
views
Which package I should use
Sequencing
Category
Sequencing
Category
updated 10.6 years ago by
Pet Chiang
▴ 30 • written 10.6 years ago by
Xiaoben Jiang
▴ 10
0
votes
7
replies
4.7k
views
Simple pathway enrichment analysis for gene lists
Microarray
Category
gage
KEGGREST
ROntoTools
Microarray
Category
gage
KEGGREST
ROntoTools
updated 10.6 years ago by
Paul Shannon
▴ 470 • written 10.6 years ago by
enricoferrero
▴ 660
0
votes
1
reply
1.4k
views
topGO analysis returns different gene counts for category than given for non-model organism
GO
Category
topGO
GO
Category
topGO
updated 10.7 years ago by
Valerie Obenchain
★ 6.8k • written 10.7 years ago by
Diana Toups Dugas
▴ 20
0
votes
0
replies
1.3k
views
new window cairo bundle Re: [Rd] R/Sweave/cairo/freetype bug fix.
Category
BEAT
Category
BEAT
10.9 years ago
Hin-Tak Leung
▴ 30
0
votes
0
replies
1.0k
views
Diff Bind consultation
Category
DiffBind
Category
DiffBind
11.0 years ago
Rory Stark
★ 5.2k
0
votes
0
replies
1.0k
views
RE : ChIPpeakAnno_2.8.0 assignCromosomeRegion
annotate
Category
ChIPpeakAnno
annotate
Category
ChIPpeakAnno
11.0 years ago
Julie Zhu
★ 4.3k
0
votes
1
reply
1.2k
views
[Rd] R/Sweave/cairo/freetype bug fix.
Category
Category
updated 11.1 years ago by
Simon Urbanek
▴ 60 • written 11.1 years ago by
Hin-Tak Leung
▴ 30
0
votes
6
replies
1.1k
views
Extract microarray data for genes identified by GO analysis
Microarray
GO
Category
Microarray
GO
Category
updated 11.2 years ago by
James W. MacDonald
65k • written 11.2 years ago by
Guest User
★ 13k
0
votes
2
replies
1.6k
views
GSEABase error parsing msigdb_v3.1.xml
GO
Infrastructure
hgu95av2
Biobase
annotate
graph
Category
AnnotationDbi
BiocGenerics
GO
updated 11.2 years ago by
Martin Morgan
25k • written 11.2 years ago by
Lina Hultin-Rosenberg
▴ 80
0
votes
2
replies
1.2k
views
Difficulties in using the mgsa package for Gene Set Analysis
GO
rat2302
Category
mgsa
GO
rat2302
Category
mgsa
updated 11.3 years ago by
Sebastian Bauer
▴ 60 • written 11.3 years ago by
Guest User
★ 13k
0
votes
0
replies
805
views
ChIPpeakAnno
Annotation
Category
ChIPpeakAnno
Annotation
Category
ChIPpeakAnno
11.4 years ago
Julie Zhu
★ 4.3k
0
votes
1
reply
899
views
HyperGTest 'count' value
Annotation
Category
Annotation
Category
11.5 years ago
Mary Kindall
▴ 70
0
votes
0
replies
698
views
strange results with edgeR::goodTuring
Category
edgeR
Category
edgeR
11.6 years ago
Gordon Smyth
50k
0
votes
2
replies
961
views
strange results with edgeR::goodTuring
Category
edgeR
Category
edgeR
updated 11.7 years ago by
Gordon Smyth
50k • written 11.7 years ago by
Francois Pepin
▴ 80
0
votes
3
replies
2.0k
views
oligo and pd.aragene.1.1.st annotation
Annotation
limma
Category
pdInfoBuilder
Annotation
limma
Category
pdInfoBuilder
updated 11.7 years ago by
Marc Carlson
★ 7.2k • written 11.7 years ago by
Stephen Rolfe
▴ 20
0
votes
2
replies
1.0k
views
easyRNAseq question
Category
DESeq
easyRNASeq
Category
DESeq
easyRNASeq
updated 11.8 years ago by
Wolfgang Huber
★ 13k • written 11.8 years ago by
Akula, Nirmala NIH/NIMH [C]
▴ 190
0
votes
3
replies
1.3k
views
GOstats - internal filtering?
Annotation
GO
hgu133plus2
GOstats
Category
Annotation
GO
hgu133plus2
GOstats
Category
updated 12.0 years ago by
James W. MacDonald
65k • written 12.0 years ago by
Andrew Jaffe
▴ 120
0
votes
0
replies
1.1k
views
Biological Pathway Database
Transcription
Pathways
Category
Transcription
Pathways
Category
12.0 years ago
Gita Singh
▴ 10
0
votes
3
replies
1.9k
views
Affymetrix Intronic Normalization Control Probes Differentially Expressed?
probe
limma
Category
probe
limma
Category
updated 12.1 years ago by
James W. MacDonald
65k • written 12.1 years ago by
Alexandra Muñoz
▴ 10
0
votes
0
replies
1.2k
views
making use of the Apis mellifera BeeBase assembly 4 data in goseq
Annotation
GO
Cancer
Apis mellifera
BSgenome
Biostrings
Category
BSgenome
rtracklayer
GO
12.1 years ago
Matthew Young
▴ 50
1
vote
0
replies
2.1k
views
TopGO p-values VS DAVID p-values
Microarray
GO
Category
topGO
Microarray
GO
Category
topGO
12.2 years ago
Paul Geeleher
★ 1.3k
0
votes
1
reply
1.6k
views
PFAM gene enrichment test using GOstats and Category
SNP
Annotation
GO
Organism
affy
GOstats
Category
SNP
Annotation
GO
Organism
affy
updated 12.3 years ago by
Davis, Wade
▴ 350 • written 12.3 years ago by
Henrik Hjarvard de Fine Licht
▴ 10
0
votes
1
reply
2.3k
views
PFAM gene enrichment test using GOstats and Category
Annotation
GO
Organism
GOstats
Category
Annotation
GO
Organism
GOstats
Category
updated 12.4 years ago by
Marc Carlson
★ 7.2k • written 12.4 years ago by
Henrik De Fine Licht
▴ 10
0
votes
2
replies
1.8k
views
retrieve the level for a GO category
GO
Category
GO
Category
updated 12.4 years ago by
Martin Morgan
25k • written 12.4 years ago by
Biase, Fernando
▴ 150
0
votes
9
replies
1.6k
views
problem with GO terms
GO
GOstats
Category
GO
GOstats
Category
updated 12.4 years ago by
James W. MacDonald
65k • written 12.4 years ago by
Ina Hoeschele
▴ 620
0
votes
0
replies
1.1k
views
goSeq error (steve Shen)
GO
Category
edgeR
goseq
GO
Category
edgeR
goseq
12.5 years ago
Alicia Oshlack
▴ 100
0
votes
4
replies
1.9k
views
edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE
limma
Category
edgeR
limma
Category
edgeR
updated 12.5 years ago by
Emanuel Heitlinger
▴ 30 • written 12.5 years ago by
Gordon Smyth
50k
0
votes
0
replies
1.1k
views
edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE
Category
edgeR
Category
edgeR
12.5 years ago
Emanuel Heitlinger
▴ 30
0
votes
0
replies
1.5k
views
I: R: R: R: Probe-level analysis of exon arrays using xps
Annotation
Normalization
Preprocessing
Breast
Prostate
probe
GLAD
Category
xps
Annotation
12.6 years ago
Lavorgna Giovanni
▴ 80
0
votes
2
replies
2.2k
views
RNA seq analysis of Arabidopsis genome
GO
Category
goseq
GO
Category
goseq
updated 12.6 years ago by
Matthew Young
▴ 50 • written 12.6 years ago by
Divya, D.
▴ 10
0
votes
4
replies
5.0k
views
goseq analysis - extracting list of my genes which are DE in the enriched GO category
GO
Category
goseq
GO
Category
goseq
updated 8.1 years ago by
darshinimamindla
▴ 10 • written 12.6 years ago by
Helen Wright
▴ 10
50 results • Page
1 of 1
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Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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