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Pathways
•
reset
0
votes
0
replies
39
views
Changing pathway names in pathway analysis
pathways
Pathways
9 days ago
Katharina
• 0
0
votes
0
replies
107
views
Job:
EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq
Transcriptomics
Pathways
Epigenetics
RNASeq
11 weeks ago
whduke
• 0
0
votes
0
replies
249
views
Pathway Analysis using GAGE
gage
RNASeq
gageData
Pathways
10 months ago
OST
• 0
1
vote
2
replies
347
views
Pathway analysis of RNAseq data using goseq package
Pathways
goseq
RNASeqData
11 months ago • updated 10 months ago
m.glymenaki
• 0
0
votes
6
replies
1.8k
views
extracting the KEGG pathway for a set of genes
Pathways
KEGG
18 months ago
Bogdan
▴ 660
0
votes
4
replies
2.9k
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
R
Pathways
pheatmap
limma
updated 22 months ago by
SamGG
▴ 290 • written 22 months ago by
r.i.s.alnuwaysir
▴ 10
1
vote
1
reply
638
views
News:
SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
SBGNview
pathways
SBGNview.data
pathview
visualization
23 months ago
Luo Weijun
★ 1.6k
2
votes
0
replies
483
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq
GO
topGO
Pathways
2.0 years ago
Ben
▴ 50
2
votes
2
replies
596
views
Pathway analysis and GO terms analysis with goseq
KEGG
Pathways
GO
goseq
updated 2.2 years ago by
James W. MacDonald
62k • written 2.2 years ago by
ojong
• 0
2
votes
1
reply
1.1k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 2.6 years ago by
Robert Castelo
★ 3.0k • written 2.6 years ago by
igor
▴ 40
0
votes
1
reply
720
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest
software error
pathways
modules
kegg
updated 2.8 years ago by
Martin Morgan
25k • written 2.8 years ago by
predeus
• 0
0
votes
4
replies
500
views
Fonction of genes/metabolites in a pathway?
gene
metabolite
functionnal annotation
pathways
updated 2.9 years ago by
Kevin Blighe
3.7k • written 2.9 years ago by
emisecherre
• 0
0
votes
0
replies
379
views
plotting Signalling Pathways using SPIA
SPIA
functional-analysis
Pathways
KEGG
2.9 years ago
Assa Yeroslaviz
★ 1.5k
2
votes
2
replies
584
views
Help for Research Proposal
drug development
pathways
bioinformatics
updated 4.2 years ago by
Steve Lianoglou
13k • written 4.2 years ago by
wajeehaejaz17
• 0
0
votes
0
replies
632
views
Pathview input error: non-numeric variable in data frame
pathview
kegg
pathways
package
4.4 years ago
anc.informatics
• 0
0
votes
0
replies
430
views
Interactive metabolic pathway
pathways
4.5 years ago
pritim2k6
• 0
0
votes
1
reply
623
views
Protein pathway analysis -- Classify, organize, and cluster a list of proteins / discovering relations between a set of proteins and linking them to …
protein
disease
pathway analysis
pathways
4.6 years ago
ረ
• 0
0
votes
0
replies
500
views
Could not find pathways in HSA gmt
pathways
gmt
4.7 years ago
flalix
• 0
0
votes
5
replies
4.0k
views
clusterProfiler: exclude pathways and add gene names to cnetplot
clusterprofiler
pathway analysis
pathways
updated 3 months ago by
yuhang
• 0 • written 4.7 years ago by
Mr.RB
▴ 20
2
votes
4
replies
1.3k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways
reactomepa
functional annotation
updated 4.7 years ago by
Guangchuang Yu
★ 1.2k • written 4.7 years ago by
martin.busch
• 0
0
votes
0
replies
663
views
Pathview web - unable to map transcriptomic data
pathways
high-throughput transcriptomics
nonmodel species
4.8 years ago
monteiro
• 0
0
votes
0
replies
638
views
igraph PoTRA error
graph
pathways
igraph
4.9 years ago
genomic8328
▴ 10
2
votes
1
reply
1.4k
views
Pathview graph with multiple states/samples or time series
Pathways
graph
Pathways
graph
updated 5.0 years ago by
atanas.kamburov
• 0 • written 9.3 years ago by
Luo Weijun
★ 1.6k
0
votes
0
replies
668
views
Two questions about pathifier package
pathways
statistics
microarray
5.1 years ago
arronar
• 0
1
vote
0
replies
909
views
Job:
Bioinformatician/Computational Biologist - Dublin City, Ireland
bioinformatician job
computational biology
genomes
pathways
machine learning
Job
5.3 years ago
bulfin.triona
▴ 10
0
votes
1
reply
1.4k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R
GSEA
GAGE
pathways
updated 5.8 years ago by
Luo Weijun
★ 1.6k • written 5.8 years ago by
snishtala03
• 0
0
votes
1
reply
1.4k
views
Pathview: visualization of data
pathways
updated 5.9 years ago by
Luo Weijun
★ 1.6k • written 5.9 years ago by
svmichaela
• 0
0
votes
0
replies
831
views
Pathway analysis for diffrential express gene
pathways
gage
annotation
gostats
6.0 years ago
avinash gupta
▴ 130
0
votes
0
replies
927
views
Job:
PhD student positions in the areas of Bioinformatics, Computer Science and Biostatistics
bioinformatician job
phd
R
pathways
Job
6.2 years ago
Frank Kramer
▴ 60
0
votes
6
replies
987
views
Is reactome.db still updated?
reactome.db
annotation
pathways
6.3 years ago
Guido Hooiveld
★ 3.5k
0
votes
4
replies
1.3k
views
EGSEA: how does the program generate the value for the up or down regulation of gene sets or pathways
pathways
gsea
egsea
gage
updated 6.4 years ago by
Monther Alhamdoosh
▴ 40 • written 6.4 years ago by
yingchen
• 0
2
votes
0
replies
1.1k
views
Job:
PhD student positions in the areas of Bioinformatics, Computer Science and Biostatistics
bioinformatician job
job
phd
R
pathways
Job
6.4 years ago
Frank Kramer
▴ 60
0
votes
2
replies
2.1k
views
WGCNA - Using real data for tutorial III
pathways
wgcna
network
rna-seq
7.1 years ago
hywel.williams
• 0
2
votes
3
replies
3.5k
views
Pathview None of the genes or compounds mapped to the pathway
pathview
pathways
KEGG
empty map
updated 18 months ago by
najib
• 0 • written 7.1 years ago by
Dani
▴ 20
2
votes
1
reply
883
views
Problem with data not found using pathview package
pathways
updated 7.7 years ago by
James W. MacDonald
62k • written 7.7 years ago by
nurhafizah.nazari
• 0
8
votes
14
replies
2.9k
views
reactome.db is not updated?
genesetenrichment
pathways
reactome.db
updated 7.8 years ago by
willem.ligtenberg
▴ 150 • written 8.2 years ago by
Guangchuang Yu
★ 1.2k
1
vote
15
replies
2.5k
views
reactome.db: reactome IDs not mapped to pathway names
annotation
pathways
updated 7.8 years ago by
willem.ligtenberg
▴ 150 • written 8.3 years ago by
Johannes Rainer
★ 2.0k
0
votes
2
replies
1.3k
views
retrieve kegg pathway abundances from gage analysis
gage
pathways
kegg
updated 7.9 years ago by
Luo Weijun
★ 1.6k • written 8.0 years ago by
francesca.defilippis
▴ 80
0
votes
13
replies
4.9k
views
gage pathways enrichment analysis
gage
pathways
kegg
updated 8.2 years ago by
Luo Weijun
★ 1.6k • written 8.2 years ago by
francesca.defilippis
▴ 80
0
votes
2
replies
3.8k
views
Pathway enrichment in bacteria metagenomes
pathways
metagenomics
updated 8.2 years ago by
Luo Weijun
★ 1.6k • written 8.2 years ago by
francesca.defilippis
▴ 80
0
votes
0
replies
1.9k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways
GO
Organism
GOstats
8.4 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
1.3k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways
GO
Organism
GOstats
8.4 years ago
Guest User
★ 12k
0
votes
0
replies
1.2k
views
Error in keggPathwayGraphs when updateCache = TRUE
Pathways
ROntoTools
Pathways
ROntoTools
8.5 years ago
Guest User
★ 12k
0
votes
0
replies
971
views
ISMB talks: Pathview for pathway-based data integration and visualization
Pathways
Visualization
pathview
Pathways
Visualization
pathview
8.6 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
808
views
ECCB 2014
Sequencing
Pathways
Sequencing
Pathways
8.7 years ago
Wolfgang Raffelsberger
▴ 60
0
votes
0
replies
1.1k
views
PostDoc opportunity
Pathways
Network
Pathways
Network
8.7 years ago
Guest User
★ 12k
0
votes
0
replies
740
views
Thalassiosira pseudonana
Annotation
Pathways
GO
Annotation
Pathways
GO
8.7 years ago
nooshin
▴ 300
0
votes
0
replies
835
views
graphite biopax conversion code?
Pathways
graphite
Pathways
graphite
8.7 years ago
Ryan C. Thompson
7.8k
0
votes
1
reply
1.1k
views
Can GAGE be used for transcript set pathway analysis
Pathways
gage
Pathways
gage
updated 8.8 years ago by
Luo Weijun
★ 1.6k • written 8.8 years ago by
sun
▴ 100
0
votes
5
replies
2.4k
views
use of voom function with attract package
Pathways
GO
attract
Pathways
GO
attract
updated 8.8 years ago by
Gordon Smyth
47k • written 8.8 years ago by
Guest User
★ 12k
50 results • Page
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Replies
Comment: DESeq2 and heatmap for multiple comparisons
by
artem.vorobyev
• 0
this I already did. My question is how to visualize differentially expressed genes on the heatmap for all 3 groups (healty->lesion->treat…
Comment: athPkgBuilder data source :missing probesets
by
nicklesteele532
• 0
> >>> > >>> How to handle the one probeset to multiple locus mappings? I can > >think 3 > >>> possible solutions: > >>> 1. pick the "best" …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
> sum(width(gr_toexclude)) [1] 2713499861 I excluded everything which was not locus. If small rna locus is from 2000 to 4000 and next locu…
Comment: Why in Bioconductor community people rarely upvote questions?
by
Hervé Pagès
16k
BTW I fail to see how the lack of upvotes to a question would be discouraging as long as you get a good answer. OTOH I can see how failing …
Answer: DESeq2 and heatmap for multiple comparisons
by
swbarnes2
★ 1.2k
If you want to know what genes are different between lesion and treated, compare them to each other.
Votes
Comment: recount 3 protect read length metadata
Answer: Doubts about manipulation and annotation of microarray files deposited at GEO
C: Batch correction in DESeq2
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
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