Showing : kegg • reset
1
vote
1
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111
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 13 days ago by 65k • written 13 days ago by ▴ 10
2
votes
13
replies
403
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
14 days ago • updated 11 days ago fernanda.backsouza ▴ 10
3
votes
2
replies
216
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 14 days ago by ★ 3.9k • written 16 days ago by ▴ 10
2
votes
2
replies
193
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
24 days ago • updated 23 days ago julia_mcdonough • 0
2
votes
2
replies
264
views
Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 11 weeks ago by ★ 3.9k • written 11 weeks ago by • 0
0
votes
0
replies
355
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
6 months ago mch • 0
0
votes
3
replies
1.2k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 7 months ago by ▴ 20 • written 7 months ago by • 0
3
votes
2
replies
1.1k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 8 months ago by ★ 3.9k • written 8 months ago by ▴ 10
0
votes
0
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354
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
9 months ago georgii.vdovin • 0
1
vote
4
replies
1.1k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
10 months ago Jiyoung Lee • 0
0
votes
1
reply
565
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 11 months ago by 41k • written 11 months ago by • 0
0
votes
5
replies
1.3k
views
enrichKEGG function error
cluster clusterProfiler KEGG
12 months ago ruba-mahmoud • 0
1
vote
3
replies
1.1k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 13 months ago by ★ 3.9k • written 13 months ago by ▴ 10
0
votes
13
replies
4.8k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
13 months ago Laia ▴ 10
0
votes
5
replies
1.2k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 13 months ago by • 0
4
votes
11
replies
2.5k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 11 months ago by • 0 • written 14 months ago by ▴ 10
4
votes
2
replies
4.4k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 14 months ago by ▴ 50 • written 14 months ago by • 0
1
vote
7
replies
1.8k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 14 months ago by ▴ 780 • written 14 months ago by ▴ 10
2
votes
6
replies
2.0k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 3 months ago by ★ 3.9k • written 14 months ago by ▴ 10
1
vote
3
replies
1.2k
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
4
votes
2
replies
1.9k
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
18 months ago Wuschel ▴ 10
0
votes
2
replies
682
views
Shivani
kegg
updated 18 months ago by ▴ 40 • written 18 months ago by • 0
3
votes
13
replies
2.6k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
20 months ago • updated 15 months ago nute11a ▴ 10
0
votes
3
replies
954
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
21 months ago abf ▴ 30
1
vote
1
reply
1.2k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG UniProt.ws
updated 21 months ago by 65k • written 21 months ago by ▴ 20
0
votes
2
replies
862
views
How do we get genes involved in all immune system pathways?
keggorthology KEGG
updated 21 months ago by ▴ 70 • written 21 months ago by ▴ 20
4
votes
6
replies
3.7k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 20 months ago by ★ 3.9k • written 22 months ago by ▴ 10
1
vote
3
replies
1.9k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 11 weeks ago by • 0 • written 23 months ago by • 0
0
votes
2
replies
3.3k
views
KEGG Pathway in R
keggrespathways KEGG
updated 23 months ago by ★ 3.9k • written 23 months ago by • 0
0
votes
1
reply
833
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.1 years ago by 41k • written 2.1 years ago by • 0
0
votes
1
reply
1.2k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 2.3 years ago by ★ 3.9k • written 2.3 years ago by • 0
0
votes
0
replies
819
views
Editing KEGG pathways in R
KEGG
2.5 years ago Jordan • 0
1
vote
0
replies
1.3k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
2.5 years ago makrez ▴ 10
1
vote
0
replies
1.3k
views
documentation on clusterProfiler output
clusterProfiler KEGG
2.6 years ago rafaela.perez ▴ 10
0
votes
6
replies
3.7k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
2.8 years ago Bogdan ▴ 670
0
votes
2
replies
2.2k
views
Can't install KEGGprofile
KEGG RNASeq
updated 2.9 years ago by 65k • written 2.9 years ago by • 0
0
votes
2
replies
1.8k
views
Drawing custom KEGG pathways
pathview KEGG
3.0 years ago • updated 2.9 years ago curiousmind007 ▴ 10
0
votes
0
replies
997
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
3.1 years ago jol.espinoz ▴ 40
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
2
votes
2
replies
1.1k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 3.4 years ago by 65k • written 3.4 years ago by • 0
0
votes
3
replies
1.1k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 3.9 years ago by 65k • written 3.9 years ago by ▴ 670
0
votes
1
reply
1.7k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 4.1 years ago by 25k • written 4.1 years ago by • 0
2
votes
2
replies
1.2k
views
Specific KEGG.db pathways not found in KEGG.db package
KEGG.db KEGG KEGGPATHNAME2ID KEGGPATHID2EXTIT
updated 4.1 years ago by 65k • written 4.1 years ago by ▴ 10
0
votes
0
replies
780
views
plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.1 years ago Assa Yeroslaviz ★ 1.5k
6
votes
6
replies
5.1k
views
Finding enriched pathways from a gene list.
microarray limma kegg ENTREZ enrichment analysis
updated 4.2 years ago by 50k • written 4.2 years ago by ▴ 50
0
votes
0
replies
883
views
gage function problem in R
gage R kegg pathview
updated 4.3 years ago by 41k • written 4.3 years ago by • 0
0
votes
2
replies
901
views
how can I find a pathway
kegg KEGGREST
4.4 years ago Bioinformatics ▴ 30
4
votes
4
replies
1.7k
views
How I interpret this plot from pathview
pathview kegg r pathway
4.5 years ago • updated 4.4 years ago AZ ▴ 30
0
votes
0
replies
958
views
KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage pathview KEGG Gene enrichment analysis
4.5 years ago MimR • 0
0
votes
0
replies
820
views
pvaluecutoff meaning in enrichKEGG
KEGG RNAseq
4.6 years ago sportiellomike • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I looked into the genomic distributions. Please see the screenshot attatched ![ distrubution for female loci, boot1 and boot2][1] how do …
Answer: How to save the DEXSeq results by Michael Love 41k
If you look at the output here: https://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.html#4_Testing_for_differe…
Answer: Method to find pathways different between 2 groups by Robert Castelo ★ 3.3k
Hi, regarding how could you combine the result from each tool, one option is using a so-called "ensembl method", for instance, the package …
Answer: Couldn't connect to server while using "pathways" by James W. MacDonald 65k
As ATpoint already noted, you should proceed from the assumption that your audience knows nothing about what you are doing, and provide eno…
Answer: Trim/Filter out-of-bounds GRanges by Michael Love 41k
https://support.bioconductor.org/p/73432/#73448
Votes
Answer: Method to find pathways different between 2 groups
Answer: Method to find pathways different between 2 groups
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
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