Showing : KEGG • reset
0
votes
13
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5.9k
views
gage pathways enrichment analysis
gage pathways kegg
updated 9.5 years ago by ★ 1.6k • written 9.5 years ago by ▴ 100
4
votes
6
replies
3.1k
views
A good alternative for RDavidWebService ??
functional annotation KEGG RDavidWebService
9.0 years ago alakatos ▴ 130
2
votes
8
replies
2.5k
views
GOseq package: Which genes are included in the "numDEInCat"?
GOseq KEGG
7.4 years ago Xavier ▴ 10
4
votes
4
replies
7.8k
views
Packages for GO and KEGG analysis on RNAseq data
GO gage goseq KEGG
updated 9.6 years ago by 50k • written 9.7 years ago by ▴ 120
0
votes
5
replies
1.9k
views
Gene set enrichment analysis for GO categories and KEGG pathway
GO KEGG
8.5 years ago libya.tahani • 0
4
votes
6
replies
3.7k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 21 months ago by ★ 4.0k • written 23 months ago by ▴ 10
0
votes
5
replies
2.7k
views
Gene Symbol with Pathview
pathview bioconductor kegg visualization
updated 8.6 years ago by ★ 1.6k • written 8.6 years ago by • 0
6
votes
5
replies
1.6k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 3.2 years ago by ★ 1.6k • written 3.2 years ago by • 0
2
votes
4
replies
1.8k
views
Can't find gene list for KEGG genesets
kegg geneset genelist gage package
updated 6.8 years ago by 50k • written 6.8 years ago by ▴ 30
2
votes
3
replies
4.9k
views
Pathview None of the genes or compounds mapped to the pathway
pathview pathways KEGG empty map
updated 2.8 years ago by • 0 • written 8.4 years ago by ▴ 20
1
vote
2
replies
2.5k
views
Error in Pathview parsing: "Parsing ./ko00195.xml file failed, please check the file!"
pathview KEGG parsing
6.5 years ago ladypurrsia ▴ 10
1
vote
3
replies
2.3k
views
Pathview pathview kegg.native=TRUE throws error in img
pathview kegg error bioconductor rnaseq
updated 6.6 years ago by ▴ 40 • written 7.2 years ago by ▴ 30
1
vote
2
replies
1.9k
views
GeneAnswer for bacteria metagenomes
geneanswers metagenome kegg
updated 7.9 years ago by ★ 1.2k • written 9.5 years ago by ▴ 100
1
vote
9
replies
2.9k
views
Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
KEGG keggrest
updated 6.1 years ago by ▴ 10 • written 6.1 years ago by ▴ 20
5
votes
4
replies
1.7k
views
Function kegga not working for species other than the conventional ones - Pathways do not overlap with universe
kegga limma pathway analysis kegg
updated 5.1 years ago by 50k • written 5.1 years ago by ▴ 60
0
votes
2
replies
1.8k
views
retrieve kegg pathway abundances from gage analysis
gage pathways kegg
updated 9.2 years ago by ★ 1.6k • written 9.2 years ago by ▴ 100
0
votes
2
replies
1.6k
views
Error when installing package gageData
gage kegg
6.3 years ago colaneri ▴ 30
1
vote
7
replies
1.9k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 15 months ago by ▴ 780 • written 15 months ago by ▴ 10
3
votes
13
replies
2.6k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
21 months ago • updated 15 months ago nute11a ▴ 10
0
votes
2
replies
1.8k
views
Drawing custom KEGG pathways
pathview KEGG
3.0 years ago curiousmind007 ▴ 10
0
votes
13
replies
5.1k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
14 months ago Laia ▴ 10
0
votes
2
replies
7.4k
views
Using Keggrest to convert ncbi gene IDs to kegg orthology and pathway
keggrest kegg keggorthology
updated 9.5 years ago by 66k • written 9.5 years ago by ▴ 100
1
vote
3
replies
1.6k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
8.3 years ago serpalma.v ▴ 60
1
vote
1
reply
1.4k
views
Highlight ECs by KEGG module
pathview KEGG
updated 6.5 years ago by ★ 1.6k • written 6.5 years ago by • 0
1
vote
1
reply
1.3k
views
embed url in pathview images
pathview r pdf kegg graphviz
updated 8.4 years ago by ★ 1.6k • written 8.4 years ago by • 0
7
votes
6
replies
3.2k
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 8.5 years ago by 50k • written 8.5 years ago by ▴ 830
2
votes
2
replies
1.2k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 3.5 years ago by 66k • written 3.5 years ago by • 0
0
votes
5
replies
2.7k
views
How to use topGO and KEGG with de-novo species
topgo edger limma kegga kegg
updated 6.7 years ago by 50k • written 6.7 years ago by ▴ 10
1
vote
4
replies
1.5k
views
Indirect path in KEGG, activation or inhibition?
bioconductor graphite kegg pathway analysis
updated 7.3 years ago by ▴ 100 • written 7.3 years ago by • 0
0
votes
2
replies
2.3k
views
Accessing KEGG (errors w/ KEGGREST)
KEGG keggrest
updated 7.4 years ago by 50k • written 7.4 years ago by • 0
0
votes
1
reply
856
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.1 years ago by 42k • written 2.1 years ago by • 0
2
votes
2
replies
283
views
Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
1
vote
3
replies
1.3k
views
Ortholog conversions of non-model organisms not present in Biomart, ensembl or KEGG
rnaseq_analysis KEGG nonmodel species
updated 5.7 years ago by 66k • written 5.7 years ago by • 0
2
votes
1
reply
1.1k
views
elim method for KEGG pathways?
KEGG genesetenrichment elim
updated 8.5 years ago by 66k • written 8.5 years ago by ▴ 40
6
votes
6
replies
5.1k
views
Finding enriched pathways from a gene list.
microarray limma kegg ENTREZ enrichment analysis
updated 4.3 years ago by 50k • written 4.3 years ago by ▴ 50
0
votes
2
replies
1.5k
views
Pathview: Exporting non native KEGG pathway ignoring same.layer argument
Pathview rgraphviz graphviz KEGG
updated 7.8 years ago by ★ 1.6k • written 7.8 years ago by ▴ 30
1
vote
1
reply
2.0k
views
Using pathview with uncommon species leads to Errors
pathview Kegg rnaseq data visualization
updated 7.9 years ago by ★ 1.6k • written 7.9 years ago by • 0
4
votes
4
replies
1.8k
views
How I interpret this plot from pathview
pathview kegg r pathway
4.5 years ago AZ ▴ 30
2
votes
2
replies
1.2k
views
Specific KEGG.db pathways not found in KEGG.db package
KEGG.db KEGG KEGGPATHNAME2ID KEGGPATHID2EXTIT
updated 4.2 years ago by 66k • written 4.2 years ago by ▴ 10
7
votes
11
replies
2.6k
views
Analysis of pathways using edgeR
rnaseq differential expression edgeR kegg
updated 6.2 years ago by 50k • written 6.2 years ago by ▴ 60
1
vote
1
reply
999
views
kegg orthology entry to pathway ko
kegg
updated 6.0 years ago by 66k • written 6.0 years ago by ▴ 10
1
vote
5
replies
3.0k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 2.9 years ago by • 0 • written 5.8 years ago by ▴ 40
1
vote
1
reply
1.1k
views
Gene Set Enrichment based on gene presence/absence
gene set enrichment KEGG
updated 6.3 years ago by ▴ 730 • written 6.3 years ago by ▴ 10
0
votes
1
reply
1.0k
views
Is there a way to specify the pathway level of classification that we want in kegga function from edgeR?
edgeR kegga KEGG
updated 5.8 years ago by 66k • written 5.8 years ago by • 0
0
votes
3
replies
1.4k
views
CHiPpeakAnno GO and/or KEGG results presenting
chippeakanno go kegg graphics
8.1 years ago lokapal • 0
1
vote
4
replies
916
views
How to apply KEGG enrichment analysis to the overlap of multiple contrasts in MArrayLM fit?
limma kegg
updated 5.7 years ago by 50k • written 5.7 years ago by ▴ 10
0
votes
3
replies
1.4k
views
kegga error from edgeR
edger r bioconductor pathway analysis kegg
updated 6.3 years ago by 50k • written 6.3 years ago by ▴ 110
0
votes
2
replies
3.5k
views
Mapping gene IDs to gene symbol of KEGG pathways with "Pathview"
Pathview KEGG annotation gene symbol visualization
updated 8.9 years ago by ★ 1.6k • written 9.0 years ago by ▴ 130
0
votes
2
replies
1.8k
views
Incomplete gene IDs in KEGG pathway testing
gostats kegg
updated 9.5 years ago by 66k • written 9.5 years ago by • 0
0
votes
1
reply
1.3k
views
KEGG with pathview using CuffDiff data
kegg readcufflinks cuffdiff cuff
updated 6.5 years ago by ▴ 160 • written 6.5 years ago by • 0
50 results • Page 1 of 1
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Comment: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Comment: conumee with Infinium MethylationEPIC v2.0 by Maximus • 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
There is the `zlibbioc` package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would requi…
Votes
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
DESeq2: add annotations (from data frame) to DESeqDataSet
Add new columns to DESeqResults from text file by matching rownames.
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