Showing : Pathview • reset
44
votes
29
replies
13k
views
.onLoad failed in loadNamespace() for 'org.Hs.eg.db'
org.Hs.eg.db pathview
updated 3.7 years ago by ▴ 130 • written 3.8 years ago by ▴ 160
0
votes
14
replies
5.5k
views
Easy way to turn OrgDb object from AnnotationHub into package?
AnnotationHub AnnotationDbi AnnotationForge pathview
7.9 years ago • updated 2.4 years ago Jenny Drnevich ★ 2.0k
3
votes
13
replies
3.2k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
2.4 years ago • updated 23 months ago nute11a ▴ 10
8
votes
13
replies
12k
views
Pathview: *** caught segfault *** cause 'memory not mapped'
pathview segfault
updated 8.5 years ago by ▴ 40 • written 9.1 years ago by ▴ 30
2
votes
11
replies
5.2k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
7.5 years ago Luo Weijun ★ 1.6k
0
votes
7
replies
2.9k
views
Error in pathview - came out of nowhere without any source code modification
pathview
updated 7.6 years ago by ★ 1.6k • written 7.7 years ago by • 0
4
votes
6
replies
4.7k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 2.4 years ago by ★ 4.1k • written 2.6 years ago by ▴ 10
0
votes
6
replies
4.3k
views
Error in using Pathview package. Do not print the pathways provided by GAGE analysis
gage pathview error
updated 8.6 years ago by ★ 1.6k • written 8.6 years ago by • 0
2
votes
6
replies
3.6k
views
Fixing download.kegg, from pathview(), which returns empty xml
pathview download.kegg() xml
updated 9.3 years ago by ★ 1.6k • written 9.4 years ago by • 0
0
votes
5
replies
2.3k
views
pathview puzzle
Pathways pathview Pathways pathview
11.4 years ago Oleg Moskvin ▴ 60
1
vote
5
replies
3.4k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 3.5 years ago by • 0 • written 6.5 years ago by ▴ 40
6
votes
5
replies
1.9k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 3.8 years ago by ★ 1.6k • written 3.8 years ago by • 0
0
votes
5
replies
3.1k
views
Gene Symbol with Pathview
pathview bioconductor kegg visualization
updated 9.2 years ago by ★ 1.6k • written 9.3 years ago by • 0
3
votes
5
replies
2.6k
views
Explanation of warning output of pathview regarding visualization of a KEGG pathway with Graphviz format
pathview clusterProfiler KEGGpath visualization Graphviz
updated 9.2 years ago by ★ 1.6k • written 9.2 years ago by ▴ 840
0
votes
5
replies
1.9k
views
How does pathview deal with enzyme with several coding genes?
RNASeq Organism pathview RNASeq Organism pathview
10.9 years ago 刘鹏飞 ▴ 80
0
votes
4
replies
2.6k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 3 months ago by • 0 • written 16 months ago by • 0
4
votes
4
replies
2.3k
views
How I interpret this plot from pathview
pathview kegg r pathway
5.2 years ago • updated 5.1 years ago AZ ▴ 30
0
votes
4
replies
1.7k
views
Argument gene.data for the correct implementation of fuction pathview of the pathview package
mroast limma pathview pathway analysis
updated 9.8 years ago by ★ 1.6k • written 9.8 years ago by ▴ 840
1
vote
4
replies
1.8k
views
Pathview error: ran fine yesterday
pathview
updated 6.6 years ago by 25k • written 7.6 years ago by ▴ 10
0
votes
4
replies
3.5k
views
Pathview for global and overview maps Re: using pathview about hsa01100
Pathways graph PROcess SIM gage pathview Pathways graph PROcess SIM gage pathview
updated 11.4 years ago by ▴ 230 • written 11.4 years ago by ★ 1.6k
1
vote
4
replies
1.6k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
19 months ago Jiyoung Lee • 0
0
votes
4
replies
2.6k
views
GAGE kegg.gsets function does not work: 'names' attribute [1] must be the same length as the vector [0]
gage pathview
9.3 years ago martin.hoelzer ▴ 20
1
vote
4
replies
380
views
pathview - multiple states
pathview Pathways KEGG
5 weeks ago Philippine • 0
0
votes
4
replies
1.5k
views
Pathview published in Bioinformatics
Visualization pathview Visualization pathview
11.6 years ago Luo Weijun ★ 1.6k
0
votes
4
replies
2.4k
views
Error: Pathway analysis using Sleuth results
pathview gage rna-seq R sleuth
8.0 years ago bioinf ▴ 10
0
votes
4
replies
3.1k
views
pathview: Warning: Download of hsa04110 xml and png files failed!
pathview
6.5 years ago masamiwata • 0
0
votes
3
replies
1.9k
views
GAGE and PATHVIEW packages
gage pathview gage pathview
updated 11.3 years ago by ★ 1.6k • written 11.3 years ago by ▴ 150
4
votes
3
replies
3.6k
views
only 0's may be mixed with negative subscripts
pathview
updated 22 months ago by ▴ 10 • written 8.1 years ago by ▴ 30
0
votes
3
replies
1.5k
views
bug report in pathview
pathview pathview
updated 10.1 years ago by • 0 • written 11.4 years ago by ★ 13k
0
votes
3
replies
1.5k
views
pathview puzzle
PROcess pathview PROcess pathview
updated 11.4 years ago by ★ 1.6k • written 11.4 years ago by ▴ 60
4
votes
3
replies
2.4k
views
Pathview: Exporting non native KEGG pathway to PNG
pathview bioconductor graphics graphviz Pathview
updated 8.3 years ago by ▴ 10 • written 8.4 years ago by ▴ 30
0
votes
3
replies
2.7k
views
Pathview -- Error in korg[ridx, coln] : subscript out of bounds
pathview korg subscript out of bounds Tutorial
updated 7.3 years ago by ★ 1.6k • written 7.3 years ago by • 0
1
vote
3
replies
1.6k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 2.1 years ago by 67k • written 2.1 years ago by • 0
1
vote
3
replies
1.9k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
8.9 years ago serpalma.v ▴ 60
2
votes
3
replies
5.4k
views
Pathview None of the genes or compounds mapped to the pathway
pathview pathways KEGG empty map
updated 3.5 years ago by • 0 • written 9.1 years ago by ▴ 20
0
votes
3
replies
2.2k
views
pathview - plotting multiple samples in the same graph?
Pathways GO pathview Pathways GO pathview
10.9 years ago Peter Davidsen ▴ 210
0
votes
3
replies
1.6k
views
None of the genes or compounds mapped to the pathway!
pathview AnnotationDbi
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
votes
3
replies
1.9k
views
Using pathview() with custom graphNEL objects
pathview mirintegrator
9.3 years ago prosomething • 0
1
vote
3
replies
2.5k
views
Pathview pathview kegg.native=TRUE throws error in img
pathview kegg error bioconductor rnaseq
updated 7.2 years ago by ▴ 40 • written 7.9 years ago by ▴ 30
0
votes
3
replies
1.4k
views
pathview: unable to use option "out.suffix"
pathview
updated 3.5 years ago by ★ 1.6k • written 3.6 years ago by • 0
1
vote
2
replies
2.0k
views
can KEGG figures produced by pathview be used in publication, or that they are copyrighted ?
pathview clusterprofiler
8.3 years ago assaf www ▴ 140
0
votes
2
replies
1.4k
views
Issue with xml files downloaded with `pathview()`
pathview kegg xml
updated 5.5 years ago by ★ 1.6k • written 5.5 years ago by ▴ 10
0
votes
2
replies
1.6k
views
Pathview: Exporting non native KEGG pathway ignoring same.layer argument
Pathview rgraphviz graphviz KEGG
updated 8.4 years ago by ★ 1.6k • written 8.4 years ago by ▴ 30
0
votes
2
replies
2.0k
views
Questions about Pathview, maybe also gage
Pathview Gage R
updated 8.0 years ago by ▴ 10 • written 8.5 years ago by • 0
0
votes
2
replies
1.8k
views
GAGE and Pathview from RNA-Seq: 'ref.idx' and 'samp.idx' when no replicates
GAGE pathview
updated 8.1 years ago by ★ 1.6k • written 8.1 years ago by ▴ 30
0
votes
2
replies
3.9k
views
Mapping gene IDs to gene symbol of KEGG pathways with "Pathview"
Pathview KEGG annotation gene symbol visualization
updated 9.6 years ago by ★ 1.6k • written 9.6 years ago by ▴ 130
1
vote
2
replies
1.7k
views
Need to convert gene IDs for GAGE pathway analysis of honey bee RNA-seq data
R gage package rnaseq pathview
8.4 years ago joanito.liberti • 0
0
votes
2
replies
2.2k
views
pathview: object 'bods' not found
pathview
updated 5.5 years ago by ▴ 10 • written 6.3 years ago by • 0
0
votes
2
replies
1.5k
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview ReactomePA
updated 4.6 years ago by 67k • written 4.6 years ago by • 0
1
vote
2
replies
2.6k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
updated 7.3 years ago by ★ 1.6k • written 7.3 years ago by • 0
50 results • Page 1 of 1
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Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000 by James W. MacDonald 67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue by k.panov • 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Comment: MBDseq analysis using qsea package by Lukas ▴ 20
Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Comment: DESeq2 analysis with transcript counts by sindhuri • 0
Thank you for the response. Currently I am using the R studio for analysis and Im running DESeq2 for analysis of the **transcript counts.ts…
Comment: iam not able to do retrive data using GEOquery R package by James W. MacDonald 67k
Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…
Votes
A: Linear regression in DESeq2
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
Answer: Issue carrying out DiffBind Analysis at a predefined peak set
Answer: Differential variability modelling with vst() expression
Answer: Differential variability modelling with vst() expression
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