Showing : pathview • reset
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Can I create a gene set using GAGE?
gage pathview gageData
4 days ago Emilia • 30
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54
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Change colors pathview
pathview
5 weeks ago da.de • 20 • updated 5 weeks ago Luo Weijun ♦ 1.5k
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4
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120
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Pathway visualization with pathview doesn't color some genes which in fact appear on the dataset
Pathways GO pathview
7 weeks ago • updated 3 days ago Emilia • 30
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66
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Job: Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
singlecellRNA-Seq pathview R statistics
7 weeks ago • updated 6 weeks ago Luo Weijun ♦ 1.5k
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92
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Pathview: empty metabolic map
pathview
3 months ago landenshanie • 40
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2
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87
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Hightlight genes/metabolites in Pathview and ReactomePA
pathview ReactomePA
6 months ago emisecherre • 0 • updated 6 months ago James W. MacDonald 55k
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50
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Pathview colors only matching ids?
pathview
6 months ago okna0215 • 0
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34
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Pathview : why are some genes not colored?
pathview rna-seq
6 months ago okna0215 • 0
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1
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257
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Argument map.symbol converting IDs even when its value is FALSE
pathview
22 months ago arthur.vinx • 0 • updated 7 months ago Kevin Blighe 2.3k
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38
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Multiple samples in pathview with different colors
pathview multiple samples
11 months ago mshofner • 0
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64
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gage function problem in R
gage R kegg pathview
11 months ago eozcan • 0 • updated 11 months ago Michael Love 31k
4
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4
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225
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How I interpret this plot from pathview
pathview kegg r pathway
14 months ago • updated 13 months ago Fereshteh • 20
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153
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KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage pathview KEGG Gene enrichment analysis
15 months ago MimR • 0
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3
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151
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None of the genes or compounds mapped to the pathway!
pathview AnnotationDbi
16 months ago kevinvdburg • 0 • updated 16 months ago Michael Love 31k
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192
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Modifying a Pathview function which needs an internet connection so that it can work without an internet connection.
Pathview Gene Mapping KEGG
16 months ago omarrafiqued • 50
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151
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pathview : kegg gene ID in the visualisation ?
pathview
17 months ago cedric.vmdl • 0
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2
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241
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Issue with xml files downloaded with `pathview()`
pathview kegg xml
18 months ago anamaria • 10 • updated 18 months ago Luo Weijun ♦ 1.5k
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2
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402
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pathview: object 'bods' not found
pathview
2.3 years ago Shi-Xiang Wang • 0 • updated 18 months ago anamaria • 10
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1
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167
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Pathview won't colour even with matching IDs
pathview
22 months ago francesco.gualdrini • 0
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172
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Help with mapping Kegg hsa01100 using pathview
kegg pathway pathview
22 months ago Ahdee • 50
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321
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Pathview input error: non-numeric variable in data frame
pathview kegg pathways package
2.3 years ago anc.informatics • 0
1
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4
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787
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KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
2.5 years ago bekah • 20 • updated 2.5 years ago Luo Weijun ♦ 1.5k
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4
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699
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pathview: Warning: Download of hsa04110 xml and png files failed!
pathview
2.5 years ago masamiwata • 0
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4
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712
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Pathview error: ran fine yesterday
pathview
3.6 years ago Epic Tinus • 10 • updated 2.6 years ago Martin Morgan 25k
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421
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Pathview results interpretation
pathview interpretation
2.6 years ago Aurora • 10
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1
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999
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Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage gage package pathview rna-seq
2.9 years ago tarun2 • 0 • updated 2.9 years ago Luo Weijun ♦ 1.5k
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427
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pathview and gage server connection issue
pathview gage pathway analysis kegg visualization
2.9 years ago Luo Weijun ♦ 1.5k
1
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1
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567
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Highlight ECs by KEGG module
pathview KEGG
3.2 years ago wrodriguez • 0 • updated 3.2 years ago Luo Weijun ♦ 1.5k
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435
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Pathview: cannot save pathway "01100"
pathview
3.2 years ago fansili2013 • 10
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Error in Pathview parsing: "Parsing ./ko00195.xml file failed, please check the file!"
pathview KEGG parsing
3.2 years ago ladypurrsia • 0
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2
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1.4k
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only 0's may be mixed with negative subscripts
pathview
4.1 years ago nature.hunger • 20 • updated 3.2 years ago map2085 • 40
1
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3
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Pathview pathview kegg.native=TRUE throws error in img
pathview kegg error bioconductor rnaseq
3.9 years ago guillermo.marco • 30 • updated 3.2 years ago map2085 • 40
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464
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Custom graphNEL object for pathview
pathview mirintegrator miRNA
3.3 years ago lech.kaczmarczyk • 10
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597
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Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
3.3 years ago JMallory • 0 • updated 3.3 years ago Luo Weijun ♦ 1.5k
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3
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794
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Pathview -- Error in korg[ridx, coln] : subscript out of bounds
pathview korg subscript out of bounds Tutorial
3.3 years ago aacevedo • 0 • updated 3.3 years ago Luo Weijun ♦ 1.5k
2
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11
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1.9k
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Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
3.5 years ago Luo Weijun ♦ 1.5k
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1
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524
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Multiple samples on the same graph
Pathview probe
3.5 years ago Luiz • 0 • updated 3.5 years ago Luo Weijun ♦ 1.5k
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438
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Get bugs from pathview package
pathview
3.6 years ago joseph • 40
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7
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1.2k
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Error in pathview - came out of nowhere without any source code modification
pathview
3.7 years ago Mataivic • 0 • updated 3.7 years ago Luo Weijun ♦ 1.5k
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2
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841
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ID unmatched in pathview
pathview
3.7 years ago joseph • 40 • updated 3.7 years ago Mataivic • 0
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629
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News: Pathview Web server published in NAR
pathway analysis visualization data integration omics pathview News
3.7 years ago Luo Weijun ♦ 1.5k
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1
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896
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error when rendering pathway with pathview package
pathview
3.7 years ago holgerbrandl • 10 • updated 3.7 years ago Luo Weijun ♦ 1.5k
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621
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How to pathway analysis of Arabidopsis thaliana organism
microarray pathview
3.9 years ago avinash gupta • 130
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683
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GAGE from DESeq: pairwise comparison between 1 reference and 3 samples
gage deseq pathview
3.9 years ago user31888 • 30
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12
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1.8k
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Easy way to turn OrgDb object from AnnotationHub into package?
AnnotationHub AnnotationDbi AnnotationForge pathview
4.0 years ago Jenny Drnevich ♦ 2.0k • updated 4.0 years ago Valerie Obenchain ♦ 6.7k
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881
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Error: Pathway analysis using Sleuth results
pathview gage rna-seq R sleuth
4.0 years ago bioinf • 10
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703
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Questions about Pathview, maybe also gage
Pathview Gage R
4.5 years ago ChIP-Tease • 0 • updated 4.1 years ago bioinf • 10
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2
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773
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GAGE and Pathview from RNA-Seq: 'ref.idx' and 'samp.idx' when no replicates
GAGE pathview
4.1 years ago user31888 • 30 • updated 4.1 years ago Luo Weijun ♦ 1.5k
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can KEGG figures produced by pathview be used in publication, or that they are copyrighted ?
pathview clusterprofiler
4.3 years ago assaf www • 140
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3
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755
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Pathview: Exporting non native KEGG pathway to PNG
pathview bioconductor graphics graphviz Pathview
4.4 years ago guillermo.marco • 30 • updated 4.3 years ago dondelelcaro • 10
122 results • Page 1 of 3
Recent ...
Replies
Comment: How to use EnrichGo of Cluster Profiler by Lluís Revilla Sancho • 610
Could you share what is the output of `head(gene)`?
Comment: DESeq2 Error: ncol(countData) == nrow(colData) is not TRUE by Pedram • 0
Hello Michael I could not make the same matrix although I did what you said
Comment: Replace a specific nucleotide sequence, at a specific position, with another in by Konstantinos Yeles • 40
Hello @Benjamin-24571 for your example, I can suggest you this code: Read <- c("1","2","3","4") Sequences <- c("ACACCCACG", "AA…
Comment: CHIP Seq Analysis by DiffBind Package by shrinka.genetics • 0
Hello Thanks for your reply. I changed my file format and now it ran. It gave one plot also. All file s are in same directory. No…
Answer: Installing Bioconductor packages in Docker by Konstantinos Yeles • 40
Hello, @adklts-21974 My way to do the installation of packages in a docker is like this: FROM bioconductor/bioconductor_docker…
Votes
A: Interpreting the results from lfcShrink() with apeglm in DESeq2
A: single-cells RNA-seq analysis by MAST with unbalanced group size
single-cells RNA-seq analysis by MAST with unbalanced group size
A: single-cells RNA-seq analysis by MAST with unbalanced group size
A: DESeq2 1.20.0 lfcshrink function
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Locations • All
Wageningen University, Wageningen, the Netherlands, 1 minute ago
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