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yeast
•
reset
0
votes
2
replies
2.0k
views
GOSim yeast
GO
Yeast
GOSim
GO
Yeast
GOSim
updated 7.1 years ago by
solis
• 0 • written 11.9 years ago by
Guest User
★ 13k
3
votes
3
replies
2.0k
views
Goseq and yeast
goseq
yeast
9.2 years ago
Marek Gierlinski
▴ 30
1
vote
2
replies
1.8k
views
GOSemSim problem for yeast proteins
GOSemSim
yeast
updated 9.2 years ago by
Guangchuang Yu
★ 1.2k • written 9.2 years ago by
horcsct
▴ 10
0
votes
0
replies
1.3k
views
mgsa vignette gives an error with the full yeast GAF
mgsa
GO
yeast
software error
9.3 years ago
nmcglincy
• 0
3
votes
4
replies
1.6k
views
ORF lengths using Yeast Annotation package
yeast
genomicranges
9.5 years ago
dktarathym
• 0
0
votes
1
reply
1.5k
views
GOseq with ce6
GO
Yeast
Organism
goseq
genomes
GO
Yeast
Organism
goseq
genomes
updated 10.0 years ago by
Nadia Davidson
▴ 310 • written 10.0 years ago by
François Lefebvre
▴ 50
0
votes
5
replies
1.7k
views
problem with makeGOGraph function
Yeast
graph
GOstats
Yeast
graph
GOstats
updated 10.1 years ago by
James W. MacDonald
65k • written 10.1 years ago by
Guest User
★ 13k
0
votes
9
replies
1.9k
views
variantAnnotation: alternative GENETIC_CODE, and circular chromosomes?
VariantAnnotation
Cancer
Yeast
annotate
Biostrings
VariantAnnotation
VariantAnnotation
updated 10.2 years ago by
Hervé Pagès
16k • written 10.2 years ago by
Janet Young
▴ 740
0
votes
1
reply
1.3k
views
I need help making a dcf seed file to encapsulate a genome assembly im using.
Cancer
Yeast
BSgenome
BSgenome
Cancer
Yeast
BSgenome
BSgenome
updated 10.3 years ago by
ashteyma@andrew.cmu.edu
▴ 10 • written 10.3 years ago by
Hervé Pagès
16k
0
votes
3
replies
1.7k
views
retrieving external Gene IDs from TranscriptDB Object
Yeast
TranscriptDb
Yeast
TranscriptDb
updated 11.0 years ago by
Ugo Borello
▴ 340 • written 11.0 years ago by
Stefanie
▴ 360
0
votes
2
replies
1.8k
views
getSequence from biomaRt changes the order of sequences given as input - is it normal?
Yeast
biomaRt
Yeast
biomaRt
updated 11.3 years ago by
Steffen Durinck
▴ 540 • written 11.3 years ago by
Emmanuel Levy
▴ 270
0
votes
0
replies
985
views
GOSim Problem
Yeast
Organism
GOSim
Yeast
Organism
GOSim
11.6 years ago
Pablo Andretta Jaskowiak
▴ 10
0
votes
0
replies
822
views
ChIPpeakAnno, callEnrichedRegions results have "holes"
Yeast
Yeast
11.6 years ago
Susan Wilson
▴ 50
0
votes
1
reply
1.1k
views
GOSemSim comparison between species
Yeast
GOSemSim
Yeast
GOSemSim
updated 11.9 years ago by
Dan Tenenbaum
★ 8.2k • written 11.9 years ago by
Katharine Coyte
▴ 10
0
votes
15
replies
2.9k
views
Rsubread crashes in 32bit linux
Yeast
Rsubread
Yeast
Rsubread
updated 11.9 years ago by
Wei Shi
★ 3.6k • written 11.9 years ago by
Robert Castelo
★ 3.3k
0
votes
2
replies
1.2k
views
oligo and pdInfoBuilder
Annotation
Yeast
oligo
pdInfoBuilder
Annotation
Yeast
oligo
pdInfoBuilder
updated 11.9 years ago by
Vincent J. Carey, Jr.
6.7k • written 11.9 years ago by
Simon Melov
▴ 340
0
votes
6
replies
1.4k
views
Questions about edgeR
Yeast
edgeR
Yeast
edgeR
updated 12.4 years ago by
Mark Robinson
▴ 880 • written 12.4 years ago by
Asma rabe
▴ 290
0
votes
0
replies
926
views
annotation package for Schizosacharomyces pombe
Annotation
Yeast
yeast2
Annotation
Yeast
yeast2
12.5 years ago
Clémentine Dressaire
▴ 120
0
votes
0
replies
1.0k
views
GetEnrichedGo term
Yeast
biomaRt
Yeast
biomaRt
12.6 years ago
Julie Zhu
★ 4.3k
0
votes
1
reply
970
views
A question about the coordinate system in the yeast database
Annotation
Yeast
Annotation
Yeast
updated 12.7 years ago by
Hervé Pagès
16k • written 12.7 years ago by
Xuekui Zhang
▴ 20
0
votes
0
replies
1.0k
views
Useful information about Ensembl release 63 mart databases
Annotation
GO
Yeast
Vega
Annotation
GO
Yeast
Vega
12.8 years ago
Rhoda Kinsella
▴ 660
0
votes
0
replies
1.7k
views
limma: multiple regression
Regression
Yeast
yeast2
limma
Regression
Yeast
yeast2
limma
12.9 years ago
Gordon Smyth
50k
0
votes
0
replies
1.2k
views
empty go terms with bioMart
GO
Yeast
probe
PROcess
biomaRt
GO
Yeast
probe
PROcess
biomaRt
13.0 years ago
chawla
▴ 190
0
votes
8
replies
2.0k
views
Rsubread alingner
Alignment
Yeast
Rsubread
Alignment
Yeast
Rsubread
13.0 years ago
Wei Shi
★ 3.6k
0
votes
2
replies
1.0k
views
Procedure
Yeast
PROcess
Yeast
PROcess
updated 13.3 years ago by
Sean Davis
21k • written 13.3 years ago by
Radhouane Aniba
▴ 240
0
votes
2
replies
1.6k
views
Flanking TSS region for reverse strand using biomaRt
Yeast
Organism
biomaRt
Yeast
Organism
biomaRt
updated 13.4 years ago by
Ania Lorenc
▴ 10 • written 13.4 years ago by
Kishor Tappita
▴ 340
0
votes
2
replies
1.4k
views
New gage package: Generally Applicable Gene-set/Pathway Analysis
Sequencing
Microarray
Pathways
GO
Yeast
gage
Sequencing
Microarray
Pathways
GO
Yeast
13.5 years ago
Luo Weijun
★ 1.6k
0
votes
1
reply
1.7k
views
Question: How does limma derives its logFC value in two colored arrays?
Yeast
affy
vsn
limma
Yeast
affy
vsn
limma
updated 13.6 years ago by
Sunny Srivastava
▴ 350 • written 13.6 years ago by
Gordon Smyth
50k
0
votes
1
reply
1.6k
views
tilingArray getting started questions
GO
Yeast
tilingArray
Starr
GO
Yeast
tilingArray
Starr
13.6 years ago
Noah Dowell
▴ 410
0
votes
1
reply
981
views
Long Time Series analysis
Microarray
Yeast
Microarray
Yeast
updated 13.7 years ago by
Xiaokuan Wei
▴ 230 • written 13.7 years ago by
boczniak767
▴ 720
0
votes
0
replies
706
views
Long Time Series analysis
Microarray
Yeast
Microarray
Yeast
13.7 years ago
Xiaokuan Wei
▴ 230
0
votes
0
replies
585
views
[limma] Separate Channel Analysis of 2 color data with summarization
Normalization
Yeast
limma
Normalization
Yeast
limma
13.7 years ago
Gordon Smyth
50k
0
votes
0
replies
1.0k
views
[limma] Separate Channel Analysis of 2 color data with summarization
Normalization
Yeast
limma
Normalization
Yeast
limma
13.7 years ago
Ana Conesa
▴ 340
0
votes
0
replies
1.8k
views
Postdoctoral positions at Harvard
Genetics
Cancer
Yeast
Genetics
Cancer
Yeast
13.7 years ago
Edo Airoldi
▴ 10
0
votes
2
replies
893
views
Regarding ScISI
Yeast
ScISI
Yeast
ScISI
updated 13.8 years ago by
Marc Carlson
★ 7.2k • written 13.8 years ago by
anupam sinha
▴ 270
0
votes
6
replies
1.6k
views
Question RE: getEnrichedGo in ChIPpeakAnno package
Yeast
ChIPpeakAnno
Starr
Yeast
ChIPpeakAnno
Starr
updated 13.9 years ago by
Julie Zhu
★ 4.3k • written 13.9 years ago by
Noah Dowell
▴ 410
0
votes
3
replies
1.3k
views
Error using getMeans function in Ringo/Starr
Yeast
probe
Ringo
Yeast
probe
Ringo
14.0 years ago
Noah Dowell
▴ 410
0
votes
2
replies
2.5k
views
org.Sc.sgd.db: Yeast ensembl ID to entrez ID conversion problem
GO
Yeast
GO
Yeast
14.1 years ago
Julie Zhu
★ 4.3k
0
votes
1
reply
1.2k
views
Help with Oligo Package: Extracting and Graphing
Transcription
Normalization
Yeast
probe
affy
graph
tilingArray
oligo
pdInfoBuilder
Starr
updated 14.5 years ago by
Tobias Straub
▴ 430 • written 14.5 years ago by
Noah Dowell
▴ 410
0
votes
2
replies
1.1k
views
YEAST package
Pathways
Yeast
Pathways
Yeast
14.6 years ago
suman Duvvuru
▴ 20
0
votes
1
reply
1.2k
views
Gene ID of yeast in GOSemSim and other GO related package may need update
Annotation
GO
Yeast
biomaRt
GOSemSim
GOSim
Annotation
GO
Yeast
biomaRt
GOSemSim
GOSim
updated 14.6 years ago by
Marc Carlson
★ 7.2k • written 14.6 years ago by
Gang Chen
▴ 20
0
votes
2
replies
1.7k
views
GO terms for E. coli micro arrays (ecoliK12.db generation)
Annotation
GO
Yeast
db0
probe
topGO
AnnotationDbi
Annotation
GO
Yeast
db0
probe
topGO
updated 14.9 years ago by
Marc Carlson
★ 7.2k • written 14.9 years ago by
Gaspard Lequeux
▴ 20
0
votes
0
replies
898
views
Gostats and custom list
Annotation
Pathways
GO
Yeast
convert
GOstats
Category
Annotation
Pathways
GO
Yeast
15.2 years ago
Iain Wallace
▴ 50
0
votes
3
replies
1.1k
views
Gostats and custom list
Annotation
Yeast
convert
GOstats
AnnotationDbi
Annotation
Yeast
convert
GOstats
updated 15.2 years ago by
Marc Carlson
★ 7.2k • written 15.2 years ago by
Iain Wallace
▴ 50
0
votes
3
replies
1.4k
views
Gostats with Yeast annotation
Microarray
Annotation
GO
Cancer
Yeast
GOstats
Microarray
Annotation
GO
Cancer
Yeast
15.2 years ago
Yolande Tra
▴ 160
0
votes
1
reply
1.2k
views
GOstats: HyperGTest for KEGG
Annotation
GO
Yeast
hgu133a
hgu133b
hgu133plus2
hgu95a
hgu95av2
hgug4110b
hgug4112a
GO
updated 15.2 years ago by
Marc Carlson
★ 7.2k • written 15.2 years ago by
Paul Evans
▴ 180
0
votes
0
replies
1.2k
views
GOstats: hyperGTest for KEGG with org.Sc.sgd.db
Annotation
GO
Yeast
hgu133a
hgu133b
hgu133plus2
hgu95a
hgu95av2
hgug4110b
hgug4112a
GO
15.3 years ago
Paul Evans
▴ 180
0
votes
0
replies
945
views
Fwd: RMA error in cdf environment with removed probes (Yeast2)
Yeast
yeast2
cdf
probe
Yeast
yeast2
cdf
probe
15.3 years ago
Omri Yahel
▴ 70
0
votes
2
replies
1.2k
views
biological reps and dye-swaps and duplicate spots in a common reference design
Yeast
limma
a4
Yeast
limma
a4
updated 15.5 years ago by
Jenny Drnevich
★ 2.0k • written 15.5 years ago by
sylvie pinloche
▴ 10
0
votes
4
replies
1.1k
views
applicability of tilingArray package
Normalization
Yeast
affy
tilingArray
Normalization
Yeast
affy
tilingArray
updated 15.5 years ago by
Wolfgang Huber
★ 13k • written 15.5 years ago by
Michael Palumbo
▴ 50
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Comment: How to retrieve gene ontology GO class?
by
bandconductor
• 0
Sorry I wasn't clear before. What I mean is the all the information associated with the go term, such as description and evidence. I have …
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
by
Michael Love
41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide
by
Gordon Smyth
50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
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You are just making up data? What is the point of this exercise?
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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