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pathview
•
reset
0
votes
0
replies
22
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
12 hours ago
Julie
• 0
0
votes
3
replies
904
views
pathview error "negative length vectors are not allowed
pathview
kegg
KEGG
updated 5 months ago by
Benji Bromberg
▴ 20 • written 6 months ago by
Mauricio Diego
• 0
0
votes
0
replies
443
views
SSL connect error in e.g. pathview from R version 4 in Windows 10
pathview
SSL
curl
8 months ago
Matthias
• 0
1
vote
4
replies
922
views
pathview - a species in KEGG pathway but not in 'korg'
pathview
KEGG
Oryza_sativa
9 months ago
Jiyoung Lee
• 0
1
vote
1
reply
1.1k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST
pathview
R
updated 11 months ago by
Guido Hooiveld
★ 3.9k • written 11 months ago by
morgan.sobol
• 0
0
votes
2
replies
1.1k
views
pathview: Warning: Failed to download KEGG xml/png files, hsa04110 skipped!
pathview
11 months ago
덕윤
• 0
4
votes
3
replies
3.1k
views
only 0's may be mixed with negative subscripts
pathview
updated 12 months ago by
saadatabu1996
▴ 10 • written 7.2 years ago by
nature.hunger
▴ 30
1
vote
3
replies
1.1k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG
TAIR_IDs
KEGGdzPathwaysGEO
pathview
updated 15 months ago by
James W. MacDonald
65k • written 15 months ago by
Arctic
• 0
4
votes
6
replies
3.4k
views
Pathview unable to download pathways
clusterProfiler
KEGGgraph
clusterpr
KEGG
pathview
updated 18 months ago by
Guido Hooiveld
★ 3.9k • written 21 months ago by
rama
▴ 10
3
votes
13
replies
2.4k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST
KEGG
gage
pathview
19 months ago • updated 13 months ago
nute11a
▴ 10
0
votes
1
reply
742
views
Pathview error Warning: Parsing ./mmu04928.xml file failed, please check the file!
KEGGgraph
pathview
updated 21 months ago by
Guido Hooiveld
★ 3.9k • written 21 months ago by
k.jane.olczak
• 0
0
votes
1
reply
1.1k
views
Help with Pathview: No annotation package for a species, gene symbols not mapped!
annotation_package
not_available_in_BioConductor
pathview
updated 17 months ago by
Rocio
• 0 • written 2.1 years ago by
bertranbio
• 0
2
votes
2
replies
956
views
pathview returns incorrect mappings for yeast
org.Sc.sgd.db
org.Sc
pathview
2.1 years ago
chase.mateusiak
• 0
0
votes
3
replies
986
views
pathview: unable to use option "out.suffix"
pathview
updated 2.7 years ago by
Luo Weijun
★ 1.6k • written 2.7 years ago by
文祥
• 0
0
votes
2
replies
1.7k
views
Drawing custom KEGG pathways
pathview
KEGG
2.8 years ago
curiousmind007
▴ 10
1
vote
2
replies
795
views
Pathview won't render some KEGG pathways
pathview
2.8 years ago
Duncan
• 0
1
vote
2
replies
1.3k
views
PATHVIEW incorrect values being plotted in output
pathview
org.Hs.eg.db
2.9 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 2.9 years ago by
Kevin Ushey
▴ 130 • written 2.9 years ago by
Arun
▴ 160
0
votes
1
reply
875
views
News:
SBGNview manuscript on bioRxiv now
pathway
SBGNview
Reactome
pathview
PANTHER
written 3.0 years ago by
Luo Weijun
★ 1.6k
0
votes
0
replies
878
views
Job:
Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
singlecellRNA-Seq
pathview
statistics
R
3.0 years ago • updated 2.9 years ago
Luo Weijun
★ 1.6k
6
votes
5
replies
1.5k
views
KEGG analysis for plasmodium
KEGG
gage
gageData
pathview
updated 3.0 years ago by
Luo Weijun
★ 1.6k • written 3.0 years ago by
MOHAMMAD
• 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
3.0 years ago
Luo Weijun
★ 1.6k
1
vote
2
replies
1.1k
views
Can I create a gene set using GAGE?
gage
pathview
gageData
written 3.2 years ago by
Emilia
▴ 30
0
votes
1
reply
767
views
Change colors pathview
pathview
updated 3.3 years ago by
Luo Weijun
★ 1.6k • written 3.3 years ago by
da.de
▴ 30
0
votes
0
replies
871
views
Job:
Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
R
statistics
pathview
singlecellRNA-Seq
3.3 years ago • updated 3.0 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
1.1k
views
Pathview: empty metabolic map
pathview
3.4 years ago
landenshanie
▴ 40
0
votes
2
replies
1.1k
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview
ReactomePA
updated 3.7 years ago by
James W. MacDonald
65k • written 3.7 years ago by
emisecherre
• 0
0
votes
0
replies
571
views
Pathview colors only matching ids?
pathview
3.7 years ago
okna0215
▴ 10
1
vote
0
replies
884
views
Pathview : why are some genes not colored?
pathview
rna-seq
3.7 years ago
okna0215
▴ 10
0
votes
1
reply
739
views
Argument map.symbol converting IDs even when its value is FALSE
pathview
updated 3.8 years ago by
Kevin Blighe
★ 3.9k • written 5.0 years ago by
arthur.vinx
• 0
0
votes
1
reply
662
views
Multiple samples in pathview with different colors
pathview
multiple samples
updated 2.8 years ago by
esteban.peguero
• 0 • written 4.1 years ago by
mshofner
• 0
0
votes
0
replies
823
views
gage function problem in R
gage
R
kegg
pathview
updated 4.1 years ago by
Michael Love
41k • written 4.1 years ago by
eozcan
• 0
4
votes
4
replies
1.6k
views
How I interpret this plot from pathview
pathview
kegg
r
pathway
4.3 years ago
AZ
▴ 30
0
votes
0
replies
921
views
KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage
pathview
KEGG
Gene enrichment analysis
4.4 years ago
MimR
• 0
0
votes
3
replies
1.2k
views
None of the genes or compounds mapped to the pathway!
pathview
AnnotationDbi
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
kevinvdburg
• 0
0
votes
0
replies
935
views
Modifying a Pathview function which needs an internet connection so that it can work without an internet connection.
Pathview
Gene Mapping
KEGG
4.5 years ago
omarrafiqued
▴ 50
0
votes
0
replies
666
views
pathview : kegg gene ID in the visualisation ?
pathview
4.6 years ago
cedric.vmdl
• 0
0
votes
2
replies
1.1k
views
Issue with xml files downloaded with `pathview()`
pathview
kegg
xml
updated 4.7 years ago by
Luo Weijun
★ 1.6k • written 4.7 years ago by
anamaria
▴ 10
0
votes
2
replies
1.7k
views
pathview: object 'bods' not found
pathview
updated 4.7 years ago by
anamaria
▴ 10 • written 5.5 years ago by
Shi-Xiang Wang
• 0
0
votes
1
reply
782
views
Pathview won't colour even with matching IDs
pathview
5.0 years ago
francesco.gualdrini
• 0
0
votes
0
replies
757
views
Help with mapping Kegg hsa01100 using pathview
kegg
pathway
pathview
5.0 years ago
Ahdee
▴ 50
0
votes
0
replies
927
views
Pathview input error: non-numeric variable in data frame
pathview
kegg
pathways
package
5.5 years ago
anc.informatics
• 0
1
vote
5
replies
2.9k
views
KEGG enrichment for non-model
kegg
pathway analysis
non-model
gage
pathview
updated 2.7 years ago by
najib
• 0 • written 5.7 years ago by
bekah
▴ 40
0
votes
4
replies
2.6k
views
pathview: Warning: Download of hsa04110 xml and png files failed!
pathview
5.7 years ago
masamiwata
• 0
1
vote
4
replies
1.5k
views
Pathview error: ran fine yesterday
pathview
updated 5.8 years ago by
Martin Morgan
25k • written 6.8 years ago by
Epic Tinus
▴ 10
0
votes
1
reply
1.6k
views
Pathview results interpretation
pathview
interpretation
5.8 years ago
Aurora
▴ 20
0
votes
2
replies
3.6k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage
gage package
pathview
rna-seq
updated 2.0 years ago by
Helen
• 0 • written 6.1 years ago by
tarun2
• 0
0
votes
0
replies
1.2k
views
pathview and gage server connection issue
pathview
gage
pathway analysis
kegg
visualization
6.1 years ago
Luo Weijun
★ 1.6k
1
vote
1
reply
1.4k
views
Highlight ECs by KEGG module
pathview
KEGG
updated 6.3 years ago by
Luo Weijun
★ 1.6k • written 6.3 years ago by
wrodriguez
• 0
0
votes
0
replies
1.1k
views
Pathview: cannot save pathway "01100"
pathview
6.3 years ago
fansili2013
▴ 50
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Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Votes
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: padj-based gradient scale from barplot (clusterProfiler results) does not work p
C: How to check that the reads in two fastq files are in the same order
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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