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38 results • Page
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Filtering for tag:
Reactome
•
reset
4
votes
3
replies
1.1k
views
Getting all gene members in a Reactome Pathway
Reactome
Bioconductor
updated 7 days ago by
darklings
▴ 220 • written 20 months ago by
The
▴ 160
0
votes
1
reply
269
views
Reactome reaction enumeration with DefinedSets
reactome
updated 7 days ago by
darklings
▴ 220 • written 17 months ago by
william.s.hayes
▴ 10
1
vote
0
replies
72
views
News:
SBGNview: Data Analysis, Integration and Visualization of All Pathways
SMPDB
PANTHER
Reactome
SBGNview
Pathview
10 days ago by
bigmawen
▴ 400
7
votes
8
replies
1.5k
views
Is there a way to visualize log fold changes for Reactome pathways in R?
pathview
RNA-Seq
reactome
bioconductor
updated 24 days ago by
bigmawen
▴ 400 • written 23 months ago by
Gabriel
▴ 90
4
votes
3
replies
1.7k
views
Graph viewer for Reactome Pathways
Reactome
R
Graph viewer
updated 7 weeks ago by
darklings
▴ 220 • written 5.9 years ago by
Deepak Tanwar
★ 4.1k
6
votes
7
replies
220
views
Diseases related pathways
pathways
wikipathway
kegg
reactome
updated 3 months ago by
xanderpico
▴ 350 • written 3 months ago by
mrashad
▴ 50
4
votes
2
replies
959
views
REVIGO equivalent for Reactome/KEGG/WikiPathways
pathway analysis
Reactome
KEGG
WikiPathways
updated 3 months ago by
ryandavidhoyle
▴ 10 • written 22 months ago by
Maciej Motyka
▴ 50
0
votes
3
replies
202
views
Obtaining directionality of pathways
Pathways
R
Reactome
Wikipathways
Bioconductor
4 months ago by
s.may-wilson
▴ 30
0
votes
0
replies
195
views
clusterProfiler gene list retrieval
clusterProfiler
GO
KEGG
Reactome
ontology
5 months ago by
LacquerHed
• 0
2
votes
3
replies
1.0k
views
How can I know when a pathway was included in Reactome?
reactome
updated 5 months ago by
darklings
▴ 220 • written 4.2 years ago by
Lluís R.
★ 1.0k
7
votes
5
replies
231
views
How to convert gallus gallus entrezID into human entrezID
R
RNA-Seq
entrezID
reactome
updated 6 months ago by
zx8754
10k • written 6 months ago by
camillab.
▴ 40
1
vote
1
reply
215
views
Are federated SPARQL queries pointless with the Pathway Commons BioPAX representation?
ontology
BioPAX
SPARQL
wikipathways
reactome
6 months ago by
mk
▴ 190
0
votes
1
reply
279
views
Why output enrichment analysis Reactome with the same gene list?
reactome
enrichment
RNA-Seq
R
enrichR
10 months ago by
camillab.
▴ 40
0
votes
1
reply
327
views
Enrichment of pathways, reactome, known networks in rice
pathway
reactome
known networks
rice
16 months ago by
zhang.jianhai
▴ 20
4
votes
6
replies
364
views
Finding the "end point" of biological pathways
pathway
automation
reactome
KEGG
17 months ago by
s.may-wilson
▴ 30
1
vote
2
replies
366
views
Comparing pathway names between online databases
Reactome
Wikipathways
KEGG
Pathways
18 months ago by
s.may-wilson
▴ 30
2
votes
4
replies
669
views
REACTOME and Ingenuity Pathway Analysis have inconsistent results
REACTOME
IPA
pathway analysis
inconsistent result
updated 19 months ago by
Buffo
★ 1.8k • written 19 months ago by
Kim
▴ 10
8
votes
5
replies
2.7k
views
How to extract protein interactions from a reactome biopax file?
Reactome
Biopax
Network
updated 19 months ago by
787685856
• 0 • written 6.2 years ago by
lovetl2002
▴ 40
0
votes
0
replies
458
views
ReactomePA only showing one pathway
ReactomePA
Reactome
22 months ago by
200dumplings
▴ 10
1
vote
1
reply
1.0k
views
Directionality of KEGG/Reactome/Wikipathways
KEGG
Reactome
pathways
wikipathways
updated 2.6 years ago by
h.mon
32k • written 2.6 years ago by
chipolino
▴ 70
0
votes
3
replies
988
views
Most genes with entrez id in KEGG database don't have a pathway assigned. Is there a tool already available that uses textmining to assign pathway to…
kegg
reactome
keggrest
3.1 years ago by
Saad Khan
▴ 400
13
votes
4
replies
1.2k
views
Tool:
iProtein.info website: Express online visualization of human genome pathways
reactome
pathway
visualization
signalling
Tool
3.3 years ago by
serena_yu
▴ 110
0
votes
0
replies
912
views
KEGG / REACTOME to SQLite ?
kegg
reactome
sqlite
sql
3.5 years ago by
G. D.
• 0
2
votes
1
reply
1.5k
views
How to download PPI network file from Reactome database for a list of genes and view them in cytoscape ?
Reactome
Cytoscape
updated 3.5 years ago by
Jean-Karim Heriche
24k • written 3.5 years ago by
anandprem1792
▴ 30
8
votes
3
replies
982
views
Programmatic obtention of SBML from a list of proteins
SBML
Reactome
Proteomics
Signaling
updated 4.1 years ago by
mhucka
▴ 50 • written 4.1 years ago by
martingarridorc
▴ 20
3
votes
5
replies
2.4k
views
Protein-protein interactions search (STRING DB)
interaction
string
reactome
updated 4.2 years ago by
cdsouthan
★ 1.8k • written 5.1 years ago by
leriapingui
▴ 20
2
votes
1
reply
2.4k
views
How to download metabolite networks from KEGG database?
metabolite
KEGG
Reactome
updated 4.7 years ago by
EagleEye
6.8k • written 4.7 years ago by
Na Sed
▴ 310
0
votes
5
replies
1.1k
views
how can i convert my gene list to a format that reactome recognises?
pathway analysis
reactome
gene
4.9 years ago by
Learner
▴ 240
1
vote
3
replies
1.6k
views
Maping reactome number to pubmed ID
pubmed
reactome
annotation
ontology
updated 5.0 years ago by
Robin Haw
▴ 160 • written 5.0 years ago by
Moses
▴ 120
2
votes
1
reply
1.0k
views
REACTOME pathways origin
REACTOME
pathway
updated 5.1 years ago by
Jean-Karim Heriche
24k • written 5.1 years ago by
ebrudermanver
▴ 80
1
vote
2
replies
1.6k
views
Map genes to Reactome pathways
reactome
pathway
genes
updated 5.2 years ago by
Jean-Karim Heriche
24k • written 5.2 years ago by
joshf
▴ 20
0
votes
0
replies
1.1k
views
Extracting all NOTCH singling target genes from available resources
gene
NOTCH
signaling pathways
kegg
reactome
updated 5.4 years ago by
Biostar
20 • written 5.5 years ago by
orzech_mag
▴ 230
0
votes
0
replies
1.8k
views
How does Reactome format pathways in BioPAX?
BioPAX
Reactome
Pathway
updated 5.5 years ago by
Biostar
20 • written 5.6 years ago by
tim.gallengor
▴ 10
1
vote
5
replies
1.9k
views
how to obtain detailed pathways?
pathway
cytoscape
reactome
KEGG
STRING
updated 5.7 years ago by
AndreiR
▴ 50 • written 5.7 years ago by
tim.gallengor
▴ 10
1
vote
1
reply
3.1k
views
Functional enrichment on orthologous groups
go
kegg
reactome
enrichment
evolution
updated 5.7 years ago by
jhc
★ 2.9k • written 5.8 years ago by
sst
▴ 20
10
votes
8
replies
2.6k
views
6 follow
List of genes to list of pathways (no enrichment)
genes
pathways
python
reactome
kegg
updated 6.7 years ago by
Newgene
▴ 360 • written 6.7 years ago by
R.Blues
▴ 130
3
votes
4
replies
2.0k
views
how to extract all the genes regulated by a specific gene ?
gene
pathway
kegg
reactome
target
updated 6.7 years ago by
Chris Evelo
10k • written 6.7 years ago by
Nicolas Rosewick
9.3k
1
vote
1
reply
1.9k
views
Extracting gene - gene Interactions From Reactome
reactome
interaction
gene
protein
updated 6.9 years ago by
pcantalupo
▴ 120 • written 6.9 years ago by
cytoscapeB
• 0
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Can't think of a particularly good alignment viewer in python. If you are more interested in result rather than doing it in python, ther…
Comment: Using outgroup in gene family dendograms
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Thank for the fast reponse. The ABC family is not the best example for this question indeed. The objective of my work is to find genes resp…
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Aye to the rushed analyses and the last-minute documentation. Horrible, but somehow it happens all the time.
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By "pooled" data, do you mean data from tissue-specific bulk-RNAseq? Or did you pool single cell (SC) RNAseq-libraries?
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What exactly do you mean by "pooled" data?
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I made a tutorial last year for University students on this topic https://www.loom.com/share/a55c1dedb8e64e7cac47f6595b751de7. Let me know …
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