Showing : Pathview • reset
0
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4
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3.2k
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Drawing custom KEGG pathways
pathview KEGG
written 4.6 years ago by ▴ 10
0
votes
1
reply
429
views
Pathview visualisation not including positive log2 fold changes
pathview Proteomics
updated 10 months ago by 68k • written 10 months ago by • 0
0
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2
replies
920
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
10 months ago ingrid.h • 0
1
vote
4
replies
942
views
pathview - multiple states
pathview Pathways KEGG
12 months ago Philippine • 0
0
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0
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517
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
19 months ago danalvoronov ▴ 10
0
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1
reply
746
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 21 months ago by ★ 4.1k • written 21 months ago by • 0
0
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4
replies
4.0k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 14 months ago by • 0 • written 2.2 years ago by • 0
0
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0
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1.3k
views
SSL connect error in e.g. pathview from R version 4 in Windows 10
pathview SSL curl
2.4 years ago Matthias • 0
1
vote
4
replies
2.2k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
2.5 years ago Jiyoung Lee • 0
1
vote
1
reply
3.3k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 2.7 years ago by ★ 4.1k • written 2.7 years ago by ▴ 10
0
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2
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2.4k
views
pathview: Warning: Failed to download KEGG xml/png files, hsa04110 skipped!
pathview
2.7 years ago 덕윤 • 0
4
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3
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4.2k
views
only 0's may be mixed with negative subscripts
pathview
updated 2.8 years ago by ▴ 10 • written 9.0 years ago by ▴ 30
1
vote
3
replies
2.1k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 3.0 years ago by 68k • written 3.1 years ago by • 0
4
votes
6
replies
5.8k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 3.3 years ago by ★ 4.1k • written 3.5 years ago by ▴ 10
3
votes
13
replies
4.2k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
3.3 years ago • updated 2.9 years ago nute11a ▴ 10
0
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1
reply
1.4k
views
Pathview error Warning: Parsing ./mmu04928.xml file failed, please check the file!
KEGGgraph pathview
updated 3.5 years ago by ★ 4.1k • written 3.5 years ago by • 0
0
votes
1
reply
1.9k
views
Help with Pathview: No annotation package for a species, gene symbols not mapped!
annotation_package not_available_in_BioConductor pathview
updated 3.2 years ago by • 0 • written 3.8 years ago by • 0
2
votes
2
replies
1.5k
views
pathview returns incorrect mappings for yeast
org.Sc.sgd.db org.Sc pathview
3.9 years ago chase.mateusiak • 0
0
votes
3
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1.8k
views
pathview: unable to use option "out.suffix"
pathview
updated 4.5 years ago by ★ 1.6k • written 4.5 years ago by • 0
1
vote
2
replies
1.3k
views
Pathview won't render some KEGG pathways
pathview
4.6 years ago Duncan • 0
1
vote
2
replies
2.5k
views
PATHVIEW incorrect values being plotted in output
pathview org.Hs.eg.db
4.7 years ago • updated 4.6 years ago Rodrigo • 0
44
votes
29
replies
14k
views
.onLoad failed in loadNamespace() for 'org.Hs.eg.db'
org.Hs.eg.db pathview
updated 4.7 years ago by ▴ 130 • written 4.7 years ago by ▴ 160
0
votes
1
reply
1.3k
views
News: SBGNview manuscript on bioRxiv now
pathway SBGNview Reactome pathview PANTHER
written 4.7 years ago by ★ 1.6k
0
votes
0
replies
1.6k
views
Job: Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
singlecellRNA-Seq pathview statistics R
4.7 years ago • updated 4.6 years ago Luo Weijun ★ 1.6k
6
votes
5
replies
2.3k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 4.8 years ago by ★ 1.6k • written 4.8 years ago by • 0
1
vote
1
reply
1.7k
views
News: SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
SBGNview pathways SBGNview.data pathview visualization
4.8 years ago Luo Weijun ★ 1.6k
1
vote
2
replies
1.7k
views
Can I create a gene set using GAGE?
gage pathview gageData
written 4.9 years ago by ▴ 40
0
votes
1
reply
1.4k
views
Change colors pathview
pathview
updated 5.0 years ago by ★ 1.6k • written 5.0 years ago by ▴ 30
0
votes
0
replies
1.3k
views
Job: Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
R statistics pathview singlecellRNA-Seq
5.1 years ago • updated 4.7 years ago Luo Weijun ★ 1.6k
0
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0
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1.6k
views
Pathview: empty metabolic map
pathview
5.2 years ago landenshanie ▴ 40
0
votes
2
replies
1.9k
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview ReactomePA
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
0
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0
replies
975
views
Pathview colors only matching ids?
pathview
5.5 years ago okna0215 ▴ 10
1
vote
0
replies
1.4k
views
Pathview : why are some genes not colored?
pathview rna-seq
5.5 years ago okna0215 ▴ 10
0
votes
1
reply
1.1k
views
Argument map.symbol converting IDs even when its value is FALSE
pathview
updated 5.6 years ago by ★ 4.0k • written 6.7 years ago by • 0
0
votes
1
reply
1.1k
views
Multiple samples in pathview with different colors
pathview multiple samples
updated 4.5 years ago by • 0 • written 5.9 years ago by • 0
0
votes
0
replies
1.3k
views
gage function problem in R
gage R kegg pathview
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
4
votes
4
replies
2.9k
views
How I interpret this plot from pathview
pathview kegg r pathway
6.1 years ago • updated 6.0 years ago AZ ▴ 30
0
votes
0
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1.5k
views
KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage pathview KEGG Gene enrichment analysis
6.2 years ago MimR • 0
0
votes
3
replies
1.9k
views
None of the genes or compounds mapped to the pathway!
pathview AnnotationDbi
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
votes
0
replies
1.4k
views
Modifying a Pathview function which needs an internet connection so that it can work without an internet connection.
Pathview Gene Mapping KEGG
6.3 years ago omarrafiqued ▴ 50
0
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0
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1.1k
views
pathview : kegg gene ID in the visualisation ?
pathview
6.4 years ago cedric.vmdl • 0
0
votes
2
replies
1.7k
views
Issue with xml files downloaded with `pathview()`
pathview kegg xml
updated 6.4 years ago by ★ 1.6k • written 6.4 years ago by ▴ 10
0
votes
2
replies
2.6k
views
pathview: object 'bods' not found
pathview
updated 6.4 years ago by ▴ 10 • written 7.3 years ago by • 0
0
votes
1
reply
1.2k
views
Pathview won't colour even with matching IDs
pathview
6.8 years ago francesco.gualdrini • 0
0
votes
0
replies
1.2k
views
Help with mapping Kegg hsa01100 using pathview
kegg pathway pathview
6.8 years ago Ahdee ▴ 60
0
votes
0
replies
1.4k
views
Pathview input error: non-numeric variable in data frame
pathview kegg pathways package
7.2 years ago anc.informatics • 0
1
vote
5
replies
4.0k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 4.4 years ago by • 0 • written 7.4 years ago by ▴ 40
0
votes
4
replies
3.4k
views
pathview: Warning: Download of hsa04110 xml and png files failed!
pathview
7.5 years ago masamiwata • 0
1
vote
4
replies
2.1k
views
Pathview error: ran fine yesterday
pathview
updated 7.5 years ago by 25k • written 8.5 years ago by ▴ 10
0
votes
1
reply
2.4k
views
Pathview results interpretation
pathview interpretation
7.6 years ago Aurora ▴ 20
146 results • Page 1 of 3
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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