Showing : Kegg • reset
4
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Packages for GO and KEGG analysis on RNAseq data
GO gage goseq KEGG
updated 8.6 years ago by 47k • written 8.7 years ago by ▴ 120
0
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2
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6.6k
views
Using Keggrest to convert ncbi gene IDs to kegg orthology and pathway
keggrest kegg keggorthology
updated 8.6 years ago by 63k • written 8.6 years ago by ▴ 100
0
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13
replies
5.1k
views
gage pathways enrichment analysis
gage pathways kegg
updated 8.5 years ago by ★ 1.6k • written 8.6 years ago by ▴ 100
6
votes
6
replies
4.2k
views
Finding enriched pathways from a gene list.
microarray limma kegg ENTREZ enrichment analysis
updated 3.3 years ago by 47k • written 3.3 years ago by ▴ 50
2
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3
replies
3.9k
views
Pathview None of the genes or compounds mapped to the pathway
pathview pathways KEGG empty map
updated 22 months ago by • 0 • written 7.5 years ago by ▴ 20
0
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2
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2.9k
views
Mapping gene IDs to gene symbol of KEGG pathways with "Pathview"
Pathview KEGG annotation gene symbol visualization
updated 8.0 years ago by ★ 1.6k • written 8.0 years ago by ▴ 120
7
votes
6
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2.8k
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 7.5 years ago by 47k • written 7.5 years ago by ▴ 810
4
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6
replies
2.6k
views
A good alternative for RDavidWebService ??
functional annotation KEGG RDavidWebService
8.0 years ago alakatos ▴ 120
0
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6
replies
2.4k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
22 months ago Bogdan ▴ 660
0
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2
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2.4k
views
KEGG Pathway in R
keggrespathways KEGG
updated 12 months ago by 3.8k • written 12 months ago by • 0
1
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5
replies
2.4k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 23 months ago by • 0 • written 4.9 years ago by ▴ 20
1
vote
9
replies
2.2k
views
Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
KEGG keggrest
updated 5.2 years ago by ▴ 10 • written 5.2 years ago by ▴ 20
0
votes
5
replies
2.1k
views
Gene Symbol with Pathview
pathview bioconductor kegg visualization
updated 7.6 years ago by ★ 1.6k • written 7.7 years ago by • 0
7
votes
11
replies
2.0k
views
Analysis of pathways using edgeR
rnaseq differential expression edgeR kegg
updated 5.3 years ago by 47k • written 5.3 years ago by ▴ 60
0
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5
replies
2.0k
views
How to use topGO and KEGG with de-novo species
topgo edger limma kegga kegg
updated 5.8 years ago by 47k • written 5.8 years ago by ▴ 10
2
votes
8
replies
2.0k
views
GOseq package: Which genes are included in the "numDEInCat"?
GOseq KEGG
6.4 years ago Xavier ▴ 10
1
vote
2
replies
2.0k
views
Error in Pathview parsing: "Parsing ./ko00195.xml file failed, please check the file!"
pathview KEGG parsing
5.6 years ago ladypurrsia ▴ 10
4
votes
6
replies
1.9k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 9 months ago by ★ 3.6k • written 11 months ago by ▴ 10
1
vote
3
replies
1.8k
views
Pathview pathview kegg.native=TRUE throws error in img
pathview kegg error bioconductor rnaseq
updated 5.6 years ago by ▴ 40 • written 6.3 years ago by ▴ 30
1
vote
1
reply
1.7k
views
Using pathview with uncommon species leads to Errors
pathview Kegg rnaseq data visualization
updated 6.9 years ago by ★ 1.6k • written 6.9 years ago by • 0
0
votes
2
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1.6k
views
Accessing KEGG (errors w/ KEGGREST)
KEGG keggrest
updated 6.4 years ago by 47k • written 6.4 years ago by • 0
1
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2
replies
1.5k
views
GeneAnswer for bacteria metagenomes
geneanswers metagenome kegg
updated 6.9 years ago by ★ 1.2k • written 8.6 years ago by ▴ 100
0
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5
replies
1.5k
views
Gene set enrichment analysis for GO categories and KEGG pathway
GO KEGG
7.5 years ago libya.tahani • 0
0
votes
2
replies
1.5k
views
Can't install KEGGprofile
KEGG RNASeq
updated 2.0 years ago by 63k • written 2.0 years ago by • 0
0
votes
2
replies
1.4k
views
Incomplete gene IDs in KEGG pathway testing
gostats kegg
updated 8.6 years ago by 63k • written 8.6 years ago by • 0
0
votes
2
replies
1.4k
views
retrieve kegg pathway abundances from gage analysis
gage pathways kegg
updated 8.3 years ago by ★ 1.6k • written 8.3 years ago by ▴ 100
4
votes
2
replies
1.3k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 3 months ago by ▴ 50 • written 3 months ago by • 0
0
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13
replies
1.2k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
9 months ago • updated 4 months ago nute11a • 0
1
vote
3
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1.2k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
7.3 years ago serpalma.v ▴ 60
0
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2
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1.2k
views
Error when installing package gageData
gage kegg
5.3 years ago colaneri ▴ 30
0
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3
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1.2k
views
CHiPpeakAnno GO and/or KEGG results presenting
chippeakanno go kegg graphics
7.2 years ago lokapal • 0
0
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2
replies
1.2k
views
Pathview: Exporting non native KEGG pathway ignoring same.layer argument
Pathview rgraphviz graphviz KEGG
updated 6.8 years ago by ★ 1.6k • written 6.8 years ago by ▴ 30
2
votes
4
replies
1.2k
views
Can't find gene list for KEGG genesets
kegg geneset genelist gage package
updated 5.8 years ago by 47k • written 5.8 years ago by ▴ 30
1
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4
replies
1.2k
views
Indirect path in KEGG, activation or inhibition?
bioconductor graphite kegg pathway analysis
updated 6.3 years ago by ▴ 100 • written 6.3 years ago by • 0
1
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2
replies
1.1k
views
How to get the latest KEGG pathway
KEGG kegg.db kegggraph
5.3 years ago Raymond ▴ 20
5
votes
4
replies
1.1k
views
Function kegga not working for species other than the conventional ones - Pathways do not overlap with universe
kegga limma pathway analysis kegg
updated 4.1 years ago by 47k • written 4.1 years ago by ▴ 60
0
votes
2
replies
1.1k
views
Drawing custom KEGG pathways
pathview KEGG
2.1 years ago • updated 2.0 years ago curiousmind007 ▴ 10
1
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1
reply
1.1k
views
Highlight ECs by KEGG module
pathview KEGG
updated 5.6 years ago by ★ 1.6k • written 5.6 years ago by • 0
0
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2
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1.1k
views
Retrieve KEGG from protein GI
R KEGG KEGGREST
6.5 years ago felipelira3 • 0
0
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3
replies
1.0k
views
kegga error from edgeR
edger r bioconductor pathway analysis kegg
updated 5.3 years ago by 47k • written 5.3 years ago by ▴ 110
0
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1
reply
1.0k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG GAGE NaN R DESeq2
updated 29 days ago by • 0 • written 4.6 years ago by • 0
6
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5
replies
1.0k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 2.2 years ago by ★ 1.6k • written 2.2 years ago by • 0
0
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0
replies
1.0k
views
ClusterProfiler - enrichKEGG on specific pathways
kegg enrichkegg clusterprofiler
4.9 years ago bekah ▴ 20
4
votes
4
replies
1.0k
views
How I interpret this plot from pathview
pathview kegg r pathway
3.6 years ago • updated 3.5 years ago AZ ▴ 30
0
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1
reply
1.0k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 3.2 years ago by 25k • written 3.2 years ago by • 0
1
vote
1
reply
999
views
embed url in pathview images
pathview r pdf kegg graphviz
updated 7.5 years ago by ★ 1.6k • written 7.5 years ago by • 0
1
vote
1
reply
988
views
How can get the GO and KEGG miRNA microarray Agilent?
go kegg limma microarray mirna
7.7 years ago santi.cabellos ▴ 10
0
votes
1
reply
977
views
Using Gage and pathview with previously processed data
pathview gage r kegg rnaseq
updated 7.3 years ago by ★ 1.6k • written 7.3 years ago by • 0
0
votes
2
replies
960
views
how to build gene.pathway data.frame for non-model organism
limma kegg topgo dataframe edger
5.8 years ago mictadlo ▴ 10
0
votes
0
replies
947
views
pathview and gage server connection issue
pathview gage pathway analysis kegg visualization
5.3 years ago Luo Weijun ★ 1.6k
50 results • Page 1 of 1
Recent ...
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Answer: Individual DESeq2 runs versus a single DESeq2 run with contrasts produce differe by ATpoint ★ 2.9k
Please see the vignette, spitting samples or keeping together is covered there. This was asked many times before, use google or the search …
Comment: Error in loadFUN(x, seqname, ranges) : trying to load regions beyond the boun by merve.sahn • 0
I guess you are mixing the NCBI and UCSC annotations. If you are using a custom-edited code to load the annotations, I would recommend clon…
Comment: HiCDCPlus extract_hic_eigenvectors() only works with larger bin sizes (> =250kb by merve.sahn • 0
Unfortunately, that seems to be your issue. There is a relevant thread [here](https://groups.google.com/g/3d-genomics/c/hVVTxXpPcxs?pli=1).
Comment: HiCDCPlus `construct_features` incompatible with BSgenome.Hsapiens.NCBI.T2T.CHM1 by merve.sahn • 0
Hi @Gemma-Zhang-326 , the package currently runs only on genomes and versions with UCSC annotations. I will need to issue an update to use …
Answer: Affymetrix analysis Chiptype hgu133plus2hsentrezg.db vs hgu133plus2.db by Guido Hooiveld ★ 3.6k
I am not familiar with Chipster, but `hgu133plus2hsentrezg.db` refers to the annotation of the Affymetrix HGU133plus2 GeneChip that is base…
Votes
Answer: How to perform a methylation analyisis from m values
A: Renaming the seqlevels in a transcript database from GenomicFeatures
A: ggbio error: Objects of type OrganismDb not supported by autoplot
Answer: DeSEQ 2 Error: some values in assay are negative
DESeq2 Error from Installing a Package
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