Showing : KEGG • reset
0
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13
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5.8k
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gage pathways enrichment analysis
gage pathways kegg
updated 9.4 years ago by ★ 1.6k • written 9.4 years ago by ▴ 100
4
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6
replies
3.1k
views
A good alternative for RDavidWebService ??
functional annotation KEGG RDavidWebService
8.9 years ago alakatos ▴ 130
2
votes
8
replies
2.4k
views
GOseq package: Which genes are included in the "numDEInCat"?
GOseq KEGG
7.3 years ago Xavier ▴ 10
4
votes
4
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7.8k
views
Packages for GO and KEGG analysis on RNAseq data
GO gage goseq KEGG
updated 9.5 years ago by 50k • written 9.6 years ago by ▴ 120
0
votes
5
replies
1.9k
views
Gene set enrichment analysis for GO categories and KEGG pathway
GO KEGG
8.4 years ago libya.tahani • 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
0
votes
5
replies
2.6k
views
Gene Symbol with Pathview
pathview bioconductor kegg visualization
updated 8.5 years ago by ★ 1.6k • written 8.5 years ago by • 0
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
4
replies
1.7k
views
Can't find gene list for KEGG genesets
kegg geneset genelist gage package
updated 6.7 years ago by 50k • written 6.7 years ago by ▴ 30
2
votes
3
replies
4.8k
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 8.3 years ago by ▴ 20
1
vote
2
replies
2.4k
views
Error in Pathview parsing: "Parsing ./ko00195.xml file failed, please check the file!"
pathview KEGG parsing
6.5 years ago • updated 6.4 years ago ladypurrsia ▴ 10
1
vote
3
replies
2.2k
views
Pathview pathview kegg.native=TRUE throws error in img
pathview kegg error bioconductor rnaseq
updated 6.5 years ago by ▴ 40 • written 7.2 years ago by ▴ 30
1
vote
2
replies
1.8k
views
GeneAnswer for bacteria metagenomes
geneanswers metagenome kegg
updated 7.8 years ago by ★ 1.2k • written 9.4 years ago by ▴ 100
1
vote
9
replies
2.9k
views
Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
KEGG keggrest
updated 6.0 years ago by ▴ 10 • written 6.0 years ago by ▴ 20
5
votes
4
replies
1.6k
views
Function kegga not working for species other than the conventional ones - Pathways do not overlap with universe
kegga limma pathway analysis kegg
updated 5.0 years ago by 50k • written 5.0 years ago by ▴ 60
0
votes
2
replies
1.7k
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
6.2 years ago colaneri ▴ 30
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
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
2
replies
1.8k
views
Drawing custom KEGG pathways
pathview KEGG
2.9 years ago curiousmind007 ▴ 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
2
replies
7.3k
views
Using Keggrest to convert ncbi gene IDs to kegg orthology and pathway
keggrest kegg keggorthology
updated 9.4 years ago by 65k • written 9.4 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
8.2 years ago serpalma.v ▴ 60
1
vote
1
reply
1.4k
views
Highlight ECs by KEGG module
pathview KEGG
updated 6.4 years ago by ★ 1.6k • written 6.4 years ago by • 0
1
vote
1
reply
1.2k
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 8.4 years ago by 50k • written 8.4 years ago by ▴ 830
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
5
replies
2.6k
views
How to use topGO and KEGG with de-novo species
topgo edger limma kegga kegg
updated 6.6 years ago by 50k • written 6.6 years ago by ▴ 10
1
vote
4
replies
1.5k
views
Indirect path in KEGG, activation or inhibition?
bioconductor graphite kegg pathway analysis
updated 7.2 years ago by ▴ 100 • written 7.2 years ago by • 0
0
votes
2
replies
2.3k
views
Accessing KEGG (errors w/ KEGGREST)
KEGG keggrest
updated 7.3 years ago by 50k • written 7.3 years 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
2
votes
2
replies
234
views
Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 9 weeks ago by ★ 3.9k • written 9 weeks 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 5.6 years ago by 65k • written 5.6 years ago by • 0
2
votes
1
reply
1.0k
views
elim method for KEGG pathways?
KEGG genesetenrichment elim
updated 8.4 years ago by 65k • written 8.4 years ago by ▴ 40
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
2
replies
1.4k
views
Pathview: Exporting non native KEGG pathway ignoring same.layer argument
Pathview rgraphviz graphviz KEGG
updated 7.7 years ago by ★ 1.6k • written 7.7 years ago by ▴ 30
1
vote
1
reply
1.9k
views
Using pathview with uncommon species leads to Errors
pathview Kegg rnaseq data visualization
updated 7.8 years ago by ★ 1.6k • written 7.8 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
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
7
votes
11
replies
2.5k
views
Analysis of pathways using edgeR
rnaseq differential expression edgeR kegg
updated 6.1 years ago by 50k • written 6.1 years ago by ▴ 60
1
vote
1
reply
975
views
kegg orthology entry to pathway ko
kegg
updated 5.9 years ago by 65k • written 5.9 years ago by ▴ 10
1
vote
5
replies
2.9k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 2.8 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 6.2 years ago by ▴ 730 • written 6.2 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 5.7 years ago by 65k • written 5.7 years ago by • 0
0
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3
replies
1.4k
views
CHiPpeakAnno GO and/or KEGG results presenting
chippeakanno go kegg graphics
8.0 years ago lokapal • 0
1
vote
4
replies
888
views
How to apply KEGG enrichment analysis to the overlap of multiple contrasts in MArrayLM fit?
limma kegg
updated 5.6 years ago by 50k • written 5.6 years ago by ▴ 10
0
votes
3
replies
1.4k
views
kegga error from edgeR
edger r bioconductor pathway analysis kegg
updated 6.2 years ago by 50k • written 6.2 years ago by ▴ 110
0
votes
2
replies
3.4k
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 8.9 years ago by ▴ 130
0
votes
2
replies
1.7k
views
Incomplete gene IDs in KEGG pathway testing
gostats kegg
updated 9.4 years ago by 65k • written 9.4 years ago by • 0
0
votes
1
reply
1.2k
views
KEGG with pathview using CuffDiff data
kegg readcufflinks cuffdiff cuff
updated 6.4 years ago by ▴ 160 • written 6.4 years ago by • 0
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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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