Showing : pathview • reset
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 3.0 years ago by ▴ 160
8
votes
13
replies
11k
views
Pathview: *** caught segfault *** cause 'memory not mapped'
pathview segfault
updated 7.8 years ago by ▴ 40 • written 8.4 years ago by ▴ 30
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
4
votes
6
replies
3.6k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 20 months ago by ★ 3.9k • written 22 months ago by ▴ 10
4
votes
3
replies
3.2k
views
only 0's may be mixed with negative subscripts
pathview
updated 14 months ago by ▴ 10 • written 7.3 years ago by ▴ 30
4
votes
3
replies
2.0k
views
Pathview: Exporting non native KEGG pathway to PNG
pathview bioconductor graphics graphviz Pathview
updated 7.6 years ago by ▴ 10 • written 7.7 years ago by ▴ 30
4
votes
4
replies
1.7k
views
How I interpret this plot from pathview
pathview kegg r pathway
4.4 years ago AZ ▴ 30
3
votes
13
replies
2.5k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
20 months ago • updated 14 months ago nute11a ▴ 10
3
votes
5
replies
2.3k
views
Explanation of warning output of pathview regarding visualization of a KEGG pathway with Graphviz format
pathview clusterProfiler KEGGpath visualization Graphviz
updated 8.4 years ago by ★ 1.6k • written 8.5 years ago by ▴ 830
2
votes
2
replies
999
views
pathview returns incorrect mappings for yeast
org.Sc.sgd.db org.Sc pathview
2.2 years ago chase.mateusiak • 0
2
votes
11
replies
4.5k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
6.8 years ago • updated 6.7 years ago Luo Weijun ★ 1.6k
2
votes
2
replies
3.0k
views
Why Pathview shows just red color (up-regulated genes) on a pathway?
Pathview pathway analysis differential gene expression
updated 7.8 years ago by ★ 1.6k • written 7.8 years ago by ▴ 10
2
votes
3
replies
4.8k
views
Pathview None of the genes or compounds mapped to the pathway
pathview pathways KEGG empty map
updated 2.8 years ago by • 0 • written 8.3 years ago by ▴ 20
2
votes
6
replies
3.3k
views
Fixing download.kegg, from pathview(), which returns empty xml
pathview download.kegg() xml
updated 8.6 years ago by ★ 1.6k • written 8.7 years ago by • 0
2
votes
2
replies
1.7k
views
Output from pathview does not seem to match input
pathview gage pathway analysis
updated 8.8 years ago by ★ 1.6k • written 8.8 years ago by • 0
1
vote
0
replies
1.7k
views
Pathview and GAGE now work with essentially all KEGG species
Visualization gage pathview Visualization gage pathview
10.5 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
1
vote
4
replies
1.5k
views
Pathview error: ran fine yesterday
pathview
updated 5.9 years ago by 25k • written 6.9 years ago by ▴ 10
1
vote
3
replies
1.1k
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
1
vote
4
replies
1.0k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
10 months ago Jiyoung Lee • 0
1
vote
2
replies
816
views
Pathview won't render some KEGG pathways
pathview
2.9 years ago Duncan • 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
3.1 years ago Luo Weijun ★ 1.6k
1
vote
5
replies
2.9k
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
1
vote
1
reply
1.4k
views
Highlight ECs by KEGG module
pathview KEGG
updated 6.4 years ago by ★ 1.6k • written 6.4 years ago by • 0
1
vote
2
replies
2.1k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
updated 6.6 years ago by ★ 1.6k • written 6.6 years ago by • 0
1
vote
2
replies
1.4k
views
PATHVIEW incorrect values being plotted in output
pathview org.Hs.eg.db
3.0 years ago Rodrigo • 0
1
vote
3
replies
2.2k
views
Pathview pathview kegg.native=TRUE throws error in img
pathview kegg error bioconductor rnaseq
updated 6.5 years ago by ▴ 40 • written 7.2 years ago by ▴ 30
1
vote
0
replies
916
views
Pathview : why are some genes not colored?
pathview rna-seq
3.8 years ago okna0215 ▴ 10
1
vote
2
replies
2.4k
views
Error in Pathview parsing: "Parsing ./ko00195.xml file failed, please check the file!"
pathview KEGG parsing
6.5 years ago • updated 6.4 years ago ladypurrsia ▴ 10
1
vote
1
reply
1.2k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 12 months ago by ★ 3.9k • written 12 months ago by • 0
1
vote
1
reply
1.7k
views
Pathview & topGO
R GO topGO pathview
updated 7.7 years ago by ★ 1.6k • written 7.7 years ago by ▴ 10
1
vote
2
replies
1.9k
views
Please help with pathway analysis using Pathview
pathview pathway analysis
updated 7.8 years ago by ★ 1.6k • written 7.8 years ago by ▴ 10
1
vote
1
reply
1.9k
views
Using pathview with uncommon species leads to Errors
pathview Kegg rnaseq data visualization
updated 7.8 years ago by ★ 1.6k • written 7.8 years ago by • 0
1
vote
1
reply
2.7k
views
Pathview color code and gene homolog handling?
pathview
updated 7.6 years ago by ★ 1.6k • written 7.6 years ago by • 0
1
vote
1
reply
1.2k
views
embed url in pathview images
pathview r pdf kegg graphviz
updated 8.4 years ago by ★ 1.6k • written 8.4 years ago by • 0
1
vote
3
replies
1.6k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
8.2 years ago serpalma.v ▴ 60
1
vote
2
replies
1.4k
views
Need to convert gene IDs for GAGE pathway analysis of honey bee RNA-seq data
R gage package rnaseq pathview
7.7 years ago joanito.liberti • 0
1
vote
0
replies
833
views
pathview should support not creating new devices
pathview
7.6 years ago dondelelcaro ▴ 10
1
vote
2
replies
1.6k
views
can KEGG figures produced by pathview be used in publication, or that they are copyrighted ?
pathview clusterprofiler
7.6 years ago assaf www ▴ 140
0
votes
3
replies
1.7k
views
GAGE and PATHVIEW packages
gage pathview gage pathview
updated 10.6 years ago by ★ 1.6k • written 10.6 years ago by ▴ 150
0
votes
0
replies
898
views
Query regarding "pathview"
pathview pathview
10.8 years ago Luo Weijun ★ 1.6k
0
votes
1
reply
1.7k
views
pathview
Organism convert pathview Organism convert pathview
updated 10.6 years ago by ★ 1.6k • written 10.6 years ago by ▴ 70
0
votes
0
replies
1.6k
views
Pathview question
KEGGREST pathview KEGGREST pathview
10.6 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
953
views
Problem running pathview due to broken XML package
GO pathview GO pathview
10.8 years ago Luo Weijun ★ 1.6k
0
votes
2
replies
1.7k
views
Questions about Pathview, maybe also gage
Pathview Gage R
updated 7.3 years ago by ▴ 10 • written 7.8 years ago by • 0
0
votes
1
reply
2.1k
views
Pathview - Problem with PNG output
Pathways graph pathview Pathways graph pathview
updated 10.6 years ago by ★ 1.6k • written 10.6 years ago by ▴ 150
0
votes
3
replies
1.3k
views
bug report in pathview
pathview pathview
updated 9.4 years ago by • 0 • written 10.6 years ago by ★ 13k
0
votes
0
replies
1.9k
views
info on pathview
graph PROcess pathview graph PROcess pathview
10.8 years ago Luo Weijun ★ 1.6k
0
votes
2
replies
3.4k
views
Mapping gene IDs to gene symbol of KEGG pathways with "Pathview"
Pathview KEGG annotation gene symbol visualization
updated 8.9 years ago by ★ 1.6k • written 8.9 years ago by ▴ 130
0
votes
0
replies
1.6k
views
Change enzyme code (EC) into gene symbol
Pathways graph pathview Pathways graph pathview
10.6 years ago Luo Weijun ★ 1.6k
50 results • Page 1 of 1
Recent ...
Replies
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Comment: minfi::read.metharray.exp by clacarion • 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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