Showing : Pathview • reset
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 4.8 years ago by ▴ 160
8
votes
13
replies
12k
views
Pathview: *** caught segfault *** cause 'memory not mapped'
pathview segfault
updated 9.5 years ago by ▴ 40 • written 10.1 years ago by ▴ 30
6
votes
5
replies
2.4k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 4.8 years ago by ★ 1.6k • written 4.8 years ago by • 0
4
votes
6
replies
6.0k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 3.4 years ago by ★ 4.1k • written 3.6 years ago by ▴ 10
4
votes
4
replies
2.9k
views
How I interpret this plot from pathview
pathview kegg r pathway
6.2 years ago • updated 6.1 years ago AZ ▴ 20
4
votes
3
replies
4.3k
views
only 0's may be mixed with negative subscripts
pathview
updated 2.9 years ago by ▴ 10 • written 9.1 years ago by ▴ 30
4
votes
3
replies
3.1k
views
Pathview: Exporting non native KEGG pathway to PNG
pathview bioconductor graphics graphviz Pathview
updated 9.3 years ago by ▴ 10 • written 9.4 years ago by ▴ 30
3
votes
13
replies
4.4k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
3.4 years ago • updated 2.9 years ago nute11a ▴ 10
3
votes
5
replies
3.3k
views
Explanation of warning output of pathview regarding visualization of a KEGG pathway with Graphviz format
pathview clusterProfiler KEGGpath visualization Graphviz
updated 10.2 years ago by ★ 1.6k • written 10.2 years ago by ▴ 840
2
votes
3
replies
6.0k
views
Pathview None of the genes or compounds mapped to the pathway
pathview pathways KEGG empty map
updated 4.5 years ago by • 0 • written 10.0 years ago by ▴ 20
2
votes
11
replies
6.1k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
8.5 years ago Luo Weijun ★ 1.6k
2
votes
2
replies
3.8k
views
Why Pathview shows just red color (up-regulated genes) on a pathway?
Pathview pathway analysis differential gene expression
updated 9.5 years ago by ★ 1.6k • written 9.6 years ago by ▴ 20
2
votes
6
replies
4.1k
views
Fixing download.kegg, from pathview(), which returns empty xml
pathview download.kegg() xml
updated 10.3 years ago by ★ 1.6k • written 10.4 years ago by • 0
2
votes
2
replies
2.3k
views
Output from pathview does not seem to match input
pathview gage pathway analysis
updated 10.5 years ago by ★ 1.6k • written 10.5 years ago by • 0
2
votes
2
replies
1.6k
views
pathview returns incorrect mappings for yeast
org.Sc.sgd.db org.Sc pathview
4.0 years ago chase.mateusiak • 0
1
vote
0
replies
2.1k
views
Pathview and GAGE now work with essentially all KEGG species
Visualization gage pathview Visualization gage pathview
12.2 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 5.0 years ago by ▴ 40
1
vote
0
replies
1.4k
views
Pathview : why are some genes not colored?
pathview rna-seq
5.6 years ago okna0215 ▴ 10
1
vote
2
replies
2.5k
views
PATHVIEW incorrect values being plotted in output
pathview org.Hs.eg.db
4.7 years ago Rodrigo • 0
1
vote
4
replies
2.3k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
2.6 years ago Jiyoung Lee • 0
1
vote
2
replies
1.3k
views
Pathview won't render some KEGG pathways
pathview
4.7 years ago Duncan • 0
1
vote
4
replies
2.1k
views
Pathview error: ran fine yesterday
pathview
updated 7.6 years ago by 25k • written 8.6 years ago by ▴ 10
1
vote
1
reply
1.8k
views
News: SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
SBGNview pathways SBGNview.data pathview visualization
4.9 years ago Luo Weijun ★ 1.6k
1
vote
5
replies
4.0k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 4.5 years ago by • 0 • written 7.5 years ago by ▴ 40
1
vote
3
replies
2.2k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
1
vote
4
replies
990
views
pathview - multiple states
pathview Pathways KEGG
13 months ago Philippine • 0
1
vote
1
reply
2.0k
views
Highlight ECs by KEGG module
pathview KEGG
updated 8.2 years ago by ★ 1.6k • written 8.2 years ago by • 0
1
vote
2
replies
3.2k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
updated 8.3 years ago by ★ 1.6k • written 8.3 years ago by • 0
1
vote
3
replies
3.0k
views
Pathview pathview kegg.native=TRUE throws error in img
pathview kegg error bioconductor rnaseq
updated 8.2 years ago by ▴ 40 • written 8.9 years ago by ▴ 30
1
vote
2
replies
3.1k
views
Error in Pathview parsing: "Parsing ./ko00195.xml file failed, please check the file!"
pathview KEGG parsing
8.2 years ago ladypurrsia ▴ 10
1
vote
1
reply
3.4k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 2.8 years ago by ★ 4.1k • written 2.8 years ago by ▴ 10
1
vote
1
reply
2.4k
views
Pathview & topGO
R GO topGO pathview
updated 9.4 years ago by ★ 1.6k • written 9.4 years ago by ▴ 10
1
vote
2
replies
2.7k
views
Please help with pathway analysis using Pathview
pathview pathway analysis
updated 9.6 years ago by ★ 1.6k • written 9.6 years ago by ▴ 20
1
vote
1
reply
2.3k
views
Using pathview with uncommon species leads to Errors
pathview Kegg rnaseq data visualization
updated 9.5 years ago by ★ 1.6k • written 9.5 years ago by • 0
1
vote
1
reply
3.4k
views
Pathview color code and gene homolog handling?
pathview
updated 9.3 years ago by ★ 1.6k • written 9.3 years ago by • 0
1
vote
1
reply
1.7k
views
embed url in pathview images
pathview r pdf kegg graphviz
updated 10.1 years ago by ★ 1.6k • written 10.1 years ago by • 0
1
vote
2
replies
1.9k
views
Need to convert gene IDs for GAGE pathway analysis of honey bee RNA-seq data
R gage package rnaseq pathview
9.4 years ago joanito.liberti • 0
1
vote
3
replies
2.3k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
9.9 years ago serpalma.v ▴ 60
1
vote
2
replies
2.5k
views
can KEGG figures produced by pathview be used in publication, or that they are copyrighted ?
pathview clusterprofiler
9.3 years ago assaf www ▴ 140
1
vote
0
replies
1.1k
views
pathview should support not creating new devices
pathview
9.3 years ago dondelelcaro ▴ 10
0
votes
3
replies
2.2k
views
GAGE and PATHVIEW packages
gage pathview gage pathview
updated 12.3 years ago by ★ 1.6k • written 12.3 years ago by ▴ 150
0
votes
0
replies
1.1k
views
Query regarding "pathview"
pathview pathview
12.5 years ago Luo Weijun ★ 1.6k
0
votes
1
reply
2.4k
views
pathview
Organism convert pathview Organism convert pathview
updated 12.3 years ago by ★ 1.6k • written 12.3 years ago by ▴ 70
0
votes
0
replies
2.0k
views
Pathview question
KEGGREST pathview KEGGREST pathview
12.3 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
1.2k
views
Problem running pathview due to broken XML package
GO pathview GO pathview
12.5 years ago Luo Weijun ★ 1.6k
0
votes
2
replies
2.3k
views
Questions about Pathview, maybe also gage
Pathview Gage R
updated 9.0 years ago by ▴ 10 • written 9.5 years ago by • 0
0
votes
1
reply
2.5k
views
Pathview - Problem with PNG output
Pathways graph pathview Pathways graph pathview
updated 12.3 years ago by ★ 1.6k • written 12.3 years ago by ▴ 150
0
votes
3
replies
1.7k
views
bug report in pathview
pathview pathview
updated 11.1 years ago by • 0 • written 12.4 years ago by ★ 13k
0
votes
0
replies
2.3k
views
info on pathview
graph PROcess pathview graph PROcess pathview
12.5 years ago Luo Weijun ★ 1.6k
0
votes
2
replies
4.7k
views
Mapping gene IDs to gene symbol of KEGG pathways with "Pathview"
Pathview KEGG annotation gene symbol visualization
updated 10.6 years ago by ★ 1.6k • written 10.6 years ago by ▴ 130
146 results • Page 1 of 3
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Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …
Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 10
You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
Comment: Incosistencies in buildSNNGraph() function by ATpoint ★ 5.0k
Just played with this a bit and I think it comes down to not having a fixed seed before running the leiden thingy. Same goes for PCA and UM…
Answer: Incosistencies in buildSNNGraph() function by Aaron Lun ★ 29k
The most obvious thing that comes to mind is the RNG seed. `cluster_leiden()` does some random number generation, somewhere deep in the **i…
Comment: Opportunity to host EuroBioC2026 Preconference workshops! by TikTsokaas33ocissalpc • 0
Thank you for sharing the EuroBioC2026 workshop opportunity. I m interested in hosting a hands on session teaching reproducible data analys…
Votes
Answer: Clarification on counting in Rsubread (featureCounts)
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
A: Conversion from counts to FPKM
Answer: Incosistencies in buildSNNGraph() function
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