Showing : KEGG • reset
0
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13
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13k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
2.7 years ago Laia ▴ 10
3
votes
13
replies
4.2k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
3.3 years ago • updated 2.9 years ago nute11a ▴ 10
0
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13
replies
7.2k
views
gage pathways enrichment analysis
gage pathways kegg
updated 11.0 years ago by ★ 1.6k • written 11.1 years ago by ▴ 100
5
votes
13
replies
4.1k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
20 months ago • updated 19 months ago fernanda.backsouza ▴ 30
7
votes
11
replies
3.5k
views
Analysis of pathways using edgeR
rnaseq differential expression edgeR kegg
updated 7.8 years ago by 53k • written 7.8 years ago by ▴ 60
4
votes
11
replies
5.4k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 2.6 years ago by • 0 • written 2.8 years ago by ▴ 10
1
vote
9
replies
4.0k
views
Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
KEGG keggrest
updated 7.7 years ago by ▴ 10 • written 7.7 years ago by ▴ 20
2
votes
8
replies
3.3k
views
GOseq package: Which genes are included in the "numDEInCat"?
GOseq KEGG
8.9 years ago Xavier ▴ 10
1
vote
7
replies
4.1k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 2.8 years ago by ▴ 780 • written 2.8 years ago by ▴ 10
4
votes
6
replies
3.9k
views
A good alternative for RDavidWebService ??
functional annotation KEGG RDavidWebService
10.5 years ago alakatos ▴ 130
7
votes
6
replies
3.8k
views
Interpretation of mroast gene set analysis in R and appropriate use of the function barcode plot regarding a microarray dataset
limma mroast barcodeplot KEGG gene set testing
updated 10.0 years ago by 53k • written 10.0 years ago by ▴ 840
6
votes
6
replies
6.3k
views
Finding enriched pathways from a gene list.
microarray limma kegg ENTREZ enrichment analysis
updated 5.8 years ago by 53k • written 5.8 years ago by ▴ 50
0
votes
6
replies
6.8k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
4.4 years ago Bogdan ▴ 670
4
votes
6
replies
5.8k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 3.3 years ago by ★ 4.1k • written 3.5 years ago by ▴ 10
2
votes
6
replies
4.8k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 23 months ago by ★ 4.1k • written 2.8 years ago by ▴ 10
0
votes
5
replies
2.9k
views
enrichKEGG function error
cluster clusterProfiler KEGG
2.7 years ago • updated 2.6 years ago ruba-mahmoud • 0
0
votes
5
replies
2.5k
views
Gene set enrichment analysis for GO categories and KEGG pathway
GO KEGG
10.0 years ago libya.tahani • 0
0
votes
5
replies
2.3k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 2.7 years ago by • 0
1
vote
5
replies
4.0k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 4.4 years ago by • 0 • written 7.4 years ago by ▴ 40
6
votes
5
replies
2.3k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 4.7 years ago by ★ 1.6k • written 4.7 years ago by • 0
0
votes
5
replies
3.6k
views
Gene Symbol with Pathview
pathview bioconductor kegg visualization
updated 10.2 years ago by ★ 1.6k • written 10.2 years ago by • 0
0
votes
5
replies
3.4k
views
How to use topGO and KEGG with de-novo species
topgo edger limma kegga kegg
updated 8.3 years ago by 53k • written 8.3 years ago by ▴ 10
1
vote
4
replies
932
views
pathview - multiple states
pathview Pathways KEGG
12 months ago Philippine • 0
1
vote
4
replies
2.2k
views
Indirect path in KEGG, activation or inhibition?
bioconductor graphite kegg pathway analysis
updated 8.8 years ago by ▴ 100 • written 8.8 years ago by • 0
2
votes
4
replies
2.7k
views
Can't find gene list for KEGG genesets
kegg geneset genelist gage package
updated 8.3 years ago by 53k • written 8.3 years ago by ▴ 30
4
votes
4
replies
2.9k
views
How I interpret this plot from pathview
pathview kegg r pathway
6.1 years ago • updated 6.0 years ago AZ ▴ 30
2
votes
4
replies
2.3k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
written 20 months ago by • 0
0
votes
4
replies
3.2k
views
Drawing custom KEGG pathways
pathview KEGG
written 4.6 years ago by ▴ 10
1
vote
4
replies
2.2k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
2.5 years ago Jiyoung Lee • 0
1
vote
4
replies
1.4k
views
How to apply KEGG enrichment analysis to the overlap of multiple contrasts in MArrayLM fit?
limma kegg
updated 7.2 years ago by 53k • written 7.2 years ago by ▴ 10
5
votes
4
replies
2.4k
views
Function kegga not working for species other than the conventional ones - Pathways do not overlap with universe
kegga limma pathway analysis kegg
updated 6.6 years ago by 53k • written 6.6 years ago by ▴ 60
4
votes
4
replies
9.3k
views
Packages for GO and KEGG analysis on RNAseq data
GO gage goseq KEGG
updated 11.2 years ago by 53k • written 11.3 years ago by ▴ 120
0
votes
4
replies
3.9k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 14 months ago by • 0 • written 2.2 years ago by • 0
2
votes
3
replies
5.9k
views
Pathview None of the genes or compounds mapped to the pathway
pathview pathways KEGG empty map
updated 4.4 years ago by • 0 • written 10.0 years ago by ▴ 20
1
vote
3
replies
3.0k
views
Pathview pathview kegg.native=TRUE throws error in img
pathview kegg error bioconductor rnaseq
updated 8.1 years ago by ▴ 40 • written 8.8 years ago by ▴ 30
1
vote
3
replies
1.9k
views
Ortholog conversions of non-model organisms not present in Biomart, ensembl or KEGG
rnaseq_analysis KEGG nonmodel species
updated 7.2 years ago by 68k • written 7.2 years ago by • 0
1
vote
3
replies
3.2k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 22 months ago by • 0 • written 3.5 years ago by • 0
1
vote
3
replies
2.1k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
0
votes
3
replies
1.6k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
3.4 years ago abf ▴ 30
1
vote
3
replies
2.4k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 2.7 years ago by ★ 4.1k • written 2.7 years ago by ▴ 10
0
votes
3
replies
1.7k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 670
0
votes
3
replies
2.0k
views
kegga error from edgeR
edger r bioconductor pathway analysis kegg
updated 7.8 years ago by 53k • written 7.8 years ago by ▴ 120
0
votes
3
replies
1.9k
views
CHiPpeakAnno GO and/or KEGG results presenting
chippeakanno go kegg graphics
9.7 years ago lokapal • 0
1
vote
3
replies
2.4k
views
Regarding the issue of background genes in enrichment analysis
KEGG goTools seqTools
written 5 months ago by ▴ 10
1
vote
3
replies
2.3k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
9.8 years ago serpalma.v ▴ 60
0
votes
3
replies
1.2k
views
pathview error
KEGGgraph KEGG
updated 18 months ago by ★ 4.1k • written 19 months ago by • 0
1
vote
2
replies
3.0k
views
Error in Pathview parsing: "Parsing ./ko00195.xml file failed, please check the file!"
pathview KEGG parsing
8.1 years ago ladypurrsia ▴ 10
1
vote
2
replies
2.5k
views
GeneAnswer for bacteria metagenomes
geneanswers metagenome kegg
updated 9.4 years ago by ★ 1.2k • written 11.1 years ago by ▴ 100
0
votes
2
replies
1.7k
views
how to build gene.pathway data.frame for non-model organism
limma kegg topgo dataframe edger
8.3 years ago mictadlo ▴ 10
0
votes
2
replies
3.8k
views
Accessing KEGG (errors w/ KEGGREST)
KEGG keggrest
updated 8.9 years ago by 53k • written 8.9 years ago by • 0
113 results • Page 1 of 3
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Comment: Question about RE-agnostic mode for intact Hi-C and Micro-C normalization(HiCDCP by TikTsoksocissalpc • 0
Normalizing complex datasets like Hi C can be challenging, much like setting up a PC for optimal gaming performance. Just as careful tuning…
Comment: p.adjust BH Question by TikTsoksocissalpc • 0
Thanks for sharing your question about RMA limma analysis While working on your experiment, it s always helpful to have some background mu…
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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