Showing : Kegg • reset
1
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53
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Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 1 day ago by 65k • written 1 day ago by ▴ 10
1
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13
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234
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
3 days ago • updated 4 hours ago fernanda.backsouza ▴ 10
3
votes
2
replies
150
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 2 days ago by ★ 3.9k • written 5 days ago by ▴ 10
2
votes
2
replies
165
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
12 days ago julia_mcdonough • 0
2
votes
2
replies
233
views
Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 9 weeks ago by ★ 3.9k • written 9 weeks ago by • 0
0
votes
0
replies
340
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
5 months ago mch • 0
0
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3
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1.1k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 6 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
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0
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339
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
9 months ago georgii.vdovin • 0
1
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4
replies
1.0k
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
552
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 10 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 • updated 11 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 12 months ago by ★ 3.9k • written 12 months ago by ▴ 10
0
votes
13
replies
4.6k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
13 months ago Laia ▴ 10
0
votes
5
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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 13 months ago by ▴ 10
4
votes
2
replies
4.3k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 13 months ago by ▴ 50 • written 13 months ago by • 0
1
vote
7
replies
1.8k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 13 months ago by ▴ 780 • written 14 months ago by ▴ 10
2
votes
6
replies
1.9k
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
1.1k
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
1.8k
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
18 months ago Wuschel ▴ 10
0
votes
2
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663
views
Shivani
kegg
updated 18 months ago by ▴ 40 • written 18 months ago by • 0
4
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6
replies
3.6k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 20 months ago by ★ 3.9k • written 22 months ago by ▴ 10
3
votes
13
replies
2.5k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
20 months ago • updated 14 months ago nute11a ▴ 10
0
votes
3
replies
940
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
20 months ago abf ▴ 30
1
vote
1
reply
1.2k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG UniProt.ws
updated 20 months ago by 65k • written 21 months ago by ▴ 20
0
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2
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840
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
1
vote
3
replies
1.8k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 9 weeks ago by • 0 • written 22 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
813
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.0 years ago by 41k • written 2.0 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 2.2 years ago by ★ 3.9k • written 2.2 years ago by • 0
0
votes
0
replies
801
views
Editing KEGG pathways in R
KEGG
2.5 years ago Jordan • 0
1
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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
1.2k
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
2.7 years ago Bogdan ▴ 670
0
votes
2
replies
1.8k
views
Drawing custom KEGG pathways
pathview KEGG
2.9 years ago curiousmind007 ▴ 10
0
votes
2
replies
2.1k
views
Can't install KEGGprofile
KEGG RNASeq
updated 2.9 years ago by 65k • written 2.9 years ago by • 0
0
votes
0
replies
982
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 4.0 years ago by 25k • written 4.0 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
770
views
plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.1 years ago Assa Yeroslaviz ★ 1.5k
3
votes
1
reply
1.2k
views
Query relating pathway enrichment analysis for DEGs using KEGG or any other database.
KEGG R offline Pathway Enrichment
updated 4.2 years ago by 50k • written 4.6 years ago by ▴ 50
6
votes
6
replies
5.0k
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
868
views
gage function problem in R
gage R kegg pathview
updated 4.2 years ago by 41k • written 4.2 years ago by • 0
4
votes
4
replies
1.7k
views
How I interpret this plot from pathview
pathview kegg r pathway
4.4 years ago AZ ▴ 30
0
votes
2
replies
892
views
how can I find a pathway
kegg KEGGREST
4.4 years ago Bioinformatics ▴ 30
0
votes
0
replies
945
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
50 results • Page 1 of 1
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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