Showing : kegg • reset
0
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0
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31
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pathview error "negative length vectors are not allowed
pathview kegg KEGG
3 days ago Mauricio Diego • 0
3
votes
2
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277
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ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 5 weeks ago by ★ 3.7k • written 5 weeks ago by ▴ 10
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0
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155
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Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
9 weeks ago georgii.vdovin • 0
1
vote
4
replies
484
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
3 months ago Jiyoung Lee • 0
0
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1
reply
325
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 3 months ago by 40k • written 3 months ago by • 0
0
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5
replies
613
views
enrichKEGG function error
cluster clusterProfiler KEGG
5 months ago • updated 4 months ago ruba-mahmoud • 0
1
vote
3
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431
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how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 5 months ago by ★ 3.7k • written 5 months ago by ▴ 10
0
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13
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1.6k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
6 months ago Laia ▴ 10
0
votes
4
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614
views
[limma::kegga] Pathway names all NA
KEGG limma
updated 10 weeks ago by • 0 • written 6 months ago by • 0
4
votes
11
replies
1.2k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 4 months ago by • 0 • written 6 months ago by ▴ 10
4
votes
2
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2.3k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 6 months ago by ▴ 50 • written 6 months ago by • 0
1
vote
7
replies
925
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 6 months ago by ▴ 720 • written 6 months ago by • 0
1
vote
4
replies
803
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
6 months ago ruiqi.li • 0
1
vote
3
replies
679
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 9 months ago by 63k • written 10 months ago by • 0
4
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2
replies
803
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
11 months ago Wuschel ▴ 10
0
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2
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429
views
Shivani
kegg
updated 11 months ago by ▴ 30 • written 11 months ago by • 0
4
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6
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2.4k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 12 months ago by ★ 3.7k • written 15 months ago by ▴ 10
3
votes
13
replies
1.7k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
13 months ago • updated 7 months ago nute11a ▴ 10
0
votes
3
replies
674
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
13 months ago abf ▴ 30
1
vote
1
reply
806
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG UniProt.ws
updated 13 months ago by 63k • written 13 months ago by ▴ 20
0
votes
2
replies
564
views
How do we get genes involved in all immune system pathways?
keggorthology KEGG
updated 13 months ago by ▴ 70 • written 14 months ago by ▴ 20
1
vote
2
replies
1.1k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 6 months ago by ▴ 10 • written 15 months ago by • 0
0
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2
replies
2.7k
views
KEGG Pathway in R
keggrespathways KEGG
updated 15 months ago by 3.8k • written 15 months ago by • 0
0
votes
1
reply
540
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 17 months ago by 40k • written 17 months ago by • 0
0
votes
1
reply
883
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 19 months ago by 3.8k • written 19 months ago by • 0
0
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0
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601
views
Editing KEGG pathways in R
KEGG
23 months ago Jordan • 0
0
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0
replies
994
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
23 months ago makrez • 0
1
vote
0
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922
views
documentation on clusterProfiler output
clusterProfiler KEGG
23 months ago rafaela.perez ▴ 10
0
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6
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2.9k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
2.1 years ago Bogdan ▴ 660
0
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2
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1.3k
views
Drawing custom KEGG pathways
pathview KEGG
2.3 years ago curiousmind007 ▴ 10
0
votes
2
replies
1.8k
views
Can't install KEGGprofile
KEGG RNASeq
updated 2.3 years ago by 63k • written 2.3 years ago by • 0
0
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0
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763
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How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
2.5 years ago jol.espinoz ▴ 40
6
votes
5
replies
1.2k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 2.5 years ago by ★ 1.6k • written 2.5 years ago by • 0
2
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2
replies
806
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 2.8 years ago by 63k • written 2.8 years ago by • 0
0
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3
replies
803
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extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 3.3 years ago by 63k • written 3.3 years ago by ▴ 660
0
votes
1
reply
1.2k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 3.4 years ago by 25k • written 3.4 years ago by • 0
2
votes
2
replies
893
views
Specific KEGG.db pathways not found in KEGG.db package
KEGG.db KEGG KEGGPATHNAME2ID KEGGPATHID2EXTIT
updated 3.5 years ago by 63k • written 3.5 years ago by ▴ 10
0
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0
replies
562
views
plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
3.5 years ago Assa Yeroslaviz ★ 1.5k
3
votes
1
reply
949
views
Query relating pathway enrichment analysis for DEGs using KEGG or any other database.
KEGG R offline Pathway Enrichment
updated 3.6 years ago by 48k • written 4.0 years ago by ▴ 50
6
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6
replies
4.6k
views
Finding enriched pathways from a gene list.
microarray limma kegg ENTREZ enrichment analysis
updated 3.6 years ago by 48k • written 3.6 years ago by ▴ 50
0
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0
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641
views
gage function problem in R
gage R kegg pathview
updated 3.6 years ago by 40k • written 3.6 years ago by • 0
4
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4
replies
1.2k
views
How I interpret this plot from pathview
pathview kegg r pathway
3.9 years ago • updated 3.8 years ago AZ ▴ 30
0
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2
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689
views
how can I find a pathway
kegg KEGGREST
3.8 years ago Bioinformatics ▴ 30
0
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0
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767
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KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage pathview KEGG Gene enrichment analysis
3.9 years ago MimR • 0
0
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0
replies
633
views
pvaluecutoff meaning in enrichKEGG
KEGG RNAseq
4.0 years ago sportiellomike • 0
0
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0
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793
views
Modifying a Pathview function which needs an internet connection so that it can work without an internet connection.
Pathview Gene Mapping KEGG
4.0 years ago omarrafiqued ▴ 50
0
votes
2
replies
926
views
Issue with xml files downloaded with `pathview()`
pathview kegg xml
updated 4.2 years ago by ★ 1.6k • written 4.2 years ago by ▴ 10
5
votes
4
replies
1.3k
views
Function kegga not working for species other than the conventional ones - Pathways do not overlap with universe
kegga limma pathway analysis kegg
updated 4.4 years ago by 48k • written 4.4 years ago by ▴ 60
0
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0
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617
views
How to integrate and visualize RNASeq / Proteomics data for metabolomics pathways?
r metabolomics KEGG Proteomics Transcriptomics
4.5 years ago Wuschel ▴ 10
0
votes
0
replies
628
views
Help with mapping Kegg hsa01100 using pathview
kegg pathway pathview
4.5 years ago Ahdee ▴ 50
50 results • Page 1 of 1
Recent ...
Replies
Comment: DMRcate design by Jitendra ▴ 10
Thanks James, do I also need to mention 'contrasts=FALSE' in cpg.annotate.And also what to mentions in analysis.type="differential",/ "ANO…
Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10
I don't know the details but do you mean using `HDF5RealizationSink` or `TENxRealizationSink` will make it possible to writing sparse multi…
Comment: DelayedArray::read_sparse_block by Koki ▴ 10
Ok, I understood. How about "writing" to HDF5? Are you going to implement `write_block_as_sparse` in `SparseArray` package?
Comment: DelayedArray::read_sparse_block by Hervé Pagès 16k
> So do you means the specification change from DelayedArray's read_sparse_block to SparseArray's read_block_as_sparse will accelerate the …
Comment: DelayedArray::read_sparse_block by Koki ▴ 10
Thanks for your reply. So do you means the specification change from `DelayedArray`'s `read_sparse_block` to `SparseArray`'s `read_block_a…
Votes
Answer: DMRcate design
Answer: DMRcate design
Comment: DMRcate design
Answer: What MetaPhlAn3 database was used in cMD 3?
Comment: Speeding up of DelayedArray::write_block()
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