Showing : Pathview • reset
0
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197
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Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 5 weeks ago by ★ 3.9k • written 6 weeks ago by • 0
0
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3
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1.2k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 7 months ago by ▴ 20 • written 7 months ago by • 0
0
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0
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528
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SSL connect error in e.g. pathview from R version 4 in Windows 10
pathview SSL curl
9 months ago Matthias • 0
1
vote
4
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1.1k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
10 months ago Jiyoung Lee • 0
1
vote
1
reply
1.3k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 12 months ago by ★ 3.9k • written 12 months ago by • 0
0
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2
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1.2k
views
pathview: Warning: Failed to download KEGG xml/png files, hsa04110 skipped!
pathview
13 months ago 덕윤 • 0
4
votes
3
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3.2k
views
only 0's may be mixed with negative subscripts
pathview
updated 14 months ago by ▴ 10 • written 7.4 years ago by ▴ 30
1
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3
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1.2k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 16 months ago by 65k • written 17 months ago by • 0
4
votes
6
replies
3.7k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 20 months ago by ★ 3.9k • written 22 months ago by ▴ 10
3
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13
replies
2.6k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
20 months ago • updated 15 months ago nute11a ▴ 10
0
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1
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794
views
Pathview error Warning: Parsing ./mmu04928.xml file failed, please check the file!
KEGGgraph pathview
updated 22 months ago by ★ 3.9k • written 23 months ago by • 0
0
votes
1
reply
1.2k
views
Help with Pathview: No annotation package for a species, gene symbols not mapped!
annotation_package not_available_in_BioConductor pathview
updated 19 months ago by • 0 • written 2.2 years ago by • 0
2
votes
2
replies
1.0k
views
pathview returns incorrect mappings for yeast
org.Sc.sgd.db org.Sc pathview
2.3 years ago chase.mateusiak • 0
0
votes
3
replies
1.1k
views
pathview: unable to use option "out.suffix"
pathview
updated 2.8 years ago by ★ 1.6k • written 2.9 years ago by • 0
0
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2
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1.8k
views
Drawing custom KEGG pathways
pathview KEGG
3.0 years ago • updated 2.9 years ago curiousmind007 ▴ 10
1
vote
2
replies
828
views
Pathview won't render some KEGG pathways
pathview
3.0 years ago Duncan • 0
1
vote
2
replies
1.5k
views
PATHVIEW incorrect values being plotted in output
pathview org.Hs.eg.db
3.0 years ago Rodrigo • 0
44
votes
29
replies
11k
views
.onLoad failed in loadNamespace() for 'org.Hs.eg.db'
org.Hs.eg.db pathview
updated 3.0 years ago by ▴ 130 • written 3.1 years ago by ▴ 160
0
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1
reply
923
views
News: SBGNview manuscript on bioRxiv now
pathway SBGNview Reactome pathview PANTHER
written 3.1 years ago by ★ 1.6k
0
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0
replies
918
views
Job: Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
singlecellRNA-Seq pathview statistics R
3.1 years ago • updated 3.0 years ago Luo Weijun ★ 1.6k
6
votes
5
replies
1.5k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 3.1 years ago by ★ 1.6k • written 3.1 years ago by • 0
1
vote
1
reply
1.1k
views
News: SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
SBGNview pathways SBGNview.data pathview visualization
3.2 years ago Luo Weijun ★ 1.6k
1
vote
2
replies
1.2k
views
Can I create a gene set using GAGE?
gage pathview gageData
written 3.3 years ago by ▴ 30
0
votes
1
reply
820
views
Change colors pathview
pathview
updated 3.4 years ago by ★ 1.6k • written 3.4 years ago by ▴ 30
0
votes
0
replies
922
views
Job: Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
R statistics pathview singlecellRNA-Seq
3.4 years ago • updated 3.1 years ago Luo Weijun ★ 1.6k
0
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0
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1.1k
views
Pathview: empty metabolic map
pathview
3.6 years ago landenshanie ▴ 40
0
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2
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1.2k
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview ReactomePA
updated 3.9 years ago by 65k • written 3.9 years ago by • 0
0
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0
replies
601
views
Pathview colors only matching ids?
pathview
3.9 years ago okna0215 ▴ 10
1
vote
0
replies
928
views
Pathview : why are some genes not colored?
pathview rna-seq
3.9 years ago okna0215 ▴ 10
0
votes
1
reply
775
views
Argument map.symbol converting IDs even when its value is FALSE
pathview
updated 3.9 years ago by ★ 3.9k • written 5.1 years ago by • 0
0
votes
1
reply
713
views
Multiple samples in pathview with different colors
pathview multiple samples
updated 2.9 years ago by • 0 • written 4.3 years ago by • 0
0
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0
replies
882
views
gage function problem in R
gage R kegg pathview
updated 4.3 years ago by 41k • written 4.3 years ago by • 0
4
votes
4
replies
1.7k
views
How I interpret this plot from pathview
pathview kegg r pathway
4.5 years ago • updated 4.4 years ago AZ ▴ 30
0
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0
replies
957
views
KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage pathview KEGG Gene enrichment analysis
4.5 years ago MimR • 0
0
votes
3
replies
1.3k
views
None of the genes or compounds mapped to the pathway!
pathview AnnotationDbi
updated 4.6 years ago by 41k • written 4.6 years ago by • 0
0
votes
0
replies
975
views
Modifying a Pathview function which needs an internet connection so that it can work without an internet connection.
Pathview Gene Mapping KEGG
4.7 years ago omarrafiqued ▴ 50
0
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0
replies
701
views
pathview : kegg gene ID in the visualisation ?
pathview
4.7 years ago cedric.vmdl • 0
0
votes
2
replies
1.2k
views
Issue with xml files downloaded with `pathview()`
pathview kegg xml
updated 4.8 years ago by ★ 1.6k • written 4.8 years ago by ▴ 10
0
votes
2
replies
1.8k
views
pathview: object 'bods' not found
pathview
updated 4.8 years ago by ▴ 10 • written 5.6 years ago by • 0
0
votes
1
reply
817
views
Pathview won't colour even with matching IDs
pathview
5.1 years ago francesco.gualdrini • 0
0
votes
0
replies
780
views
Help with mapping Kegg hsa01100 using pathview
kegg pathway pathview
5.2 years ago Ahdee ▴ 50
0
votes
0
replies
962
views
Pathview input error: non-numeric variable in data frame
pathview kegg pathways package
5.6 years ago anc.informatics • 0
1
vote
5
replies
3.0k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 2.8 years ago by • 0 • written 5.8 years ago by ▴ 40
0
votes
4
replies
2.7k
views
pathview: Warning: Download of hsa04110 xml and png files failed!
pathview
5.8 years ago masamiwata • 0
1
vote
4
replies
1.6k
views
Pathview error: ran fine yesterday
pathview
updated 5.9 years ago by 25k • written 6.9 years ago by ▴ 10
0
votes
1
reply
1.6k
views
Pathview results interpretation
pathview interpretation
5.9 years ago Aurora ▴ 20
0
votes
2
replies
3.7k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage gage package pathview rna-seq
updated 2.2 years ago by • 0 • written 6.2 years ago by • 0
0
votes
0
replies
1.3k
views
pathview and gage server connection issue
pathview gage pathway analysis kegg visualization
6.2 years ago Luo Weijun ★ 1.6k
1
vote
1
reply
1.4k
views
Highlight ECs by KEGG module
pathview KEGG
updated 6.5 years ago by ★ 1.6k • written 6.5 years ago by • 0
0
votes
0
replies
1.1k
views
Pathview: cannot save pathway "01100"
pathview
6.5 years ago fansili2013 ▴ 50
50 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
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Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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