Showing : Pathway analysis • reset
8
votes
4
replies
1.7k
views
NaN results on some pathways in CAMERA
camera edger pathway analysis
updated 8.9 years ago by 50k • written 8.9 years ago by ★ 7.9k
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 5.0 years ago by 50k • written 5.0 years ago by ▴ 60
4
votes
7
replies
1.9k
views
Issues uploading database for metabolomic data analysis with Pathway Activity Profiling - PAPi
papi metabolomics pathway analysis
updated 7.2 years ago by ▴ 10 • written 8.1 years ago by ▴ 10
4
votes
7
replies
7.4k
views
Comparison between two different group's pathway analysis results
gage DESeq2 pathway analysis
updated 4.7 years ago by ▴ 270 • written 4.7 years ago by ▴ 10
3
votes
2
replies
4.9k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 6.5 years ago by ★ 1.2k • written 6.5 years ago by ▴ 10
2
votes
11
replies
4.5k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
6.8 years ago Luo Weijun ★ 1.6k
2
votes
2
replies
1.7k
views
Output from pathview does not seem to match input
pathview gage pathway analysis
updated 8.8 years ago by ★ 1.6k • written 8.8 years ago by • 0
2
votes
2
replies
3.1k
views
Why Pathview shows just red color (up-regulated genes) on a pathway?
Pathview pathway analysis differential gene expression
updated 7.9 years ago by ★ 1.6k • written 7.9 years ago by ▴ 10
2
votes
6
replies
1.7k
views
Appropriate use of the function mroast to find KEGG pathways for differential expression
mroast limma pathway analysis differential gene expression affymetrix
9.1 years ago svlachavas ▴ 830
2
votes
3
replies
2.0k
views
Why are there so many not annotated probes in the PorGene-1_1-st affymetrix array?
affymetrix microarrays pd.porgene.1.1.st annotation probe to gene id pathway analysis
updated 8.3 years ago by 65k • written 8.3 years ago by ▴ 60
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
1
vote
0
replies
2.1k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
6.2 years ago digrigor ▴ 10
1
vote
1
reply
1.2k
views
Python Module from Kim and Volsky (2005) PAGE: Parametric Analysis of Gene Set Enrichment paper?
GSEA PAGE microarray differential gene expression pathway analysis
updated 7.1 years ago by ★ 4.0k • written 7.1 years ago by • 0
1
vote
1
reply
1.1k
views
DESeq2 function in interpreting the differential expression results in terms of higher order biological processes or molecular pathways
pathway analysis deseq2
updated 7.0 years ago by 42k • written 7.0 years ago by • 0
1
vote
5
replies
3.0k
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
3
replies
1.4k
views
Pathway analysis from list of differentially expressed genes with fold change, pvalues and normalised expression levels in R
rnaseq pathway analysis R limma
updated 6.5 years ago by ▴ 730 • written 6.5 years ago by • 0
1
vote
2
replies
2.4k
views
(Gene-set)Pathway analysis based on network/pathway topology in R
SPIA functional enrichment pathway topology pathway analysis bioconductor
8.8 years ago svlachavas ▴ 830
1
vote
2
replies
1.9k
views
Please help with pathway analysis using Pathview
pathview pathway analysis
updated 7.9 years ago by ★ 1.6k • written 7.9 years ago by ▴ 10
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
2
replies
1.4k
views
KEGG data error?
bioconductor graphite pathway analysis
updated 7.2 years ago by ▴ 100 • written 7.2 years ago by • 0
0
votes
1
reply
996
views
Protein pathway analysis -- Classify, organize, and cluster a list of proteins / discovering relations between a set of proteins and linking them to …
protein disease pathway analysis pathways
5.8 years ago ረ • 0
0
votes
0
replies
719
views
master gene list for pathway analysis
pathway analysis sigpathway Genesets_EntrezGeneIDs.RData
5.6 years ago maria • 0
0
votes
0
replies
577
views
Pathviews for DE list of genes
pathviews RNAseq Pathway analysis
updated 4.6 years ago by 42k • written 4.6 years ago by • 0
0
votes
1
reply
2.1k
views
SPIA error - names of de are not in reference array
SPIA named vectors pathway analysis
updated 21 months ago by • 0 • written 9.5 years ago by • 0
0
votes
3
replies
1.3k
views
Pathway analysis of bacterial RNA-seq data
annotation rna-seq pathway analysis
3.6 years ago microPhD • 0
0
votes
4
replies
1.6k
views
Argument gene.data for the correct implementation of fuction pathview of the pathview package
mroast limma pathview pathway analysis
updated 9.1 years ago by ★ 1.6k • written 9.1 years ago by ▴ 830
0
votes
0
replies
1.3k
views
Error with R package RontoTools regarding administrator issues downloading updated KEGG data
ROntoTools Rstudio bioconductor administratorIssues pathway analysis
8.6 years ago svlachavas ▴ 830
0
votes
0
replies
1.6k
views
Pathview Web Server: user friendly pathway visualization and data integration
pathview pathway analysis visualization web server omics data
8.4 years ago Weijun Luo • 0
0
votes
3
replies
3.7k
views
Gene ontology and pathway analysis in R - replicate ToppGene features; best strategy for getting annotations?
topgo biomart gene ontology goexpress pathway analysis
updated 8.0 years ago by ▴ 350 • written 8.0 years ago by ▴ 120
0
votes
0
replies
1.3k
views
gene over-representation analysis with custom background
pathway analysis over-representation analysis DAVID pantherDB consensuspathDB
7.4 years ago smt8n • 0
0
votes
4
replies
1.3k
views
DESeq2 normalization prior to identification of highly-expressed functional categories
deseq2 pathway analysis order normalization
updated 7.4 years ago by 42k • written 7.4 years ago by • 0
0
votes
3
replies
2.3k
views
topGO - treating up- and down-regulated genes separately
topGO GSEA pathway analysis
updated 7.2 years ago by ▴ 730 • written 7.2 years ago by • 0
0
votes
0
replies
1.5k
views
News: Pathview Web server published in NAR
pathway analysis visualization data integration omics pathview News
7.0 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
1.1k
views
SPIA Package : Activated and Inhibited
SPIA R pathway analysis
6.9 years ago khhgng • 0
0
votes
0
replies
1.2k
views
Problem about functional annotation network of WGCNA modules (modified)
wgcna network analysis pathway analysis
6.9 years ago panagiotis.mokos ▴ 40
0
votes
1
reply
1.7k
views
PANTHER.db- external pointer error
goseq pantherdb pathway analysis gene ontology
updated 6.4 years ago by 65k • written 6.4 years ago by ▴ 10
0
votes
1
reply
1.1k
views
How to identify Disease biomarkers " DNA sequences as biomarkers "
dnaseq pathway analysis protein biomarkers
6.3 years ago emadelhewihy • 0
0
votes
0
replies
1.3k
views
pathview and gage server connection issue
pathview gage pathway analysis kegg visualization
6.3 years ago Luo Weijun ★ 1.6k
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
0
replies
1.2k
views
miR2Pathway Finite Observations
pathway analysis mirna parallel
6.2 years ago genomic8328 ▴ 10
0
votes
3
replies
1.3k
views
Collapsing transcript counts into pathways / gene lists with DESeq2
deseq2 pathway analysis tximport
updated 6.2 years ago by 42k • written 6.2 years ago by • 0
0
votes
0
replies
943
views
SPIA function error in ToPASeq
ToPASeq SPIA pathway analysis R
6.1 years ago fawazfebin ▴ 60
0
votes
5
replies
5.8k
views
clusterProfiler: exclude pathways and add gene names to cnetplot
clusterprofiler pathway analysis pathways
updated 18 months ago by • 0 • written 6.0 years ago by ▴ 20
0
votes
0
replies
1.1k
views
'names' attribute must be the same length as the vector - PAPi problems
PAPi metabolomics pathway analysis raphael
5.8 years ago maryke.wijma • 0
44 results • Page 1 of 1
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Comment: Create protein sequences including variants from a VCF file by Yun • 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization? by Daniel • 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Guido Hooiveld ★ 4.0k
FWIW: based on [previous posts][1] it is suggested to install like this: install.packages(pkgs="./org.Vdahliae.eg.db", repos=NULL, typ…
Votes
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
Answer: SGSeq: moving toward diffex from SGSeq analysis
Answer: How to design DEXSeq formula for multiple variables
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