Showing : pathway analysis • reset
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3
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Pathway analysis of bacterial RNA-seq data
annotation rna-seq pathway analysis
3.0 years ago microPhD • 0
0
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0
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441
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Pathviews for DE list of genes
pathviews RNAseq Pathway analysis
updated 3.9 years ago by 40k • written 3.9 years ago by • 0
4
votes
7
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5.3k
views
Comparison between two different group's pathway analysis results
gage DESeq2 pathway analysis
updated 4.1 years ago by ▴ 270 • written 4.1 years ago by ▴ 10
5
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4
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1.3k
views
Function kegga not working for species other than the conventional ones - Pathways do not overlap with universe
kegga limma pathway analysis kegg
updated 4.4 years ago by 48k • written 4.4 years ago by ▴ 60
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586
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master gene list for pathway analysis
pathway analysis sigpathway Genesets_EntrezGeneIDs.RData
5.0 years ago maria • 0
1
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5
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2.5k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 2.2 years ago by • 0 • written 5.2 years ago by ▴ 20
0
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1
reply
777
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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
5.2 years ago ረ • 0
0
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0
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830
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'names' attribute must be the same length as the vector - PAPi problems
PAPi metabolomics pathway analysis raphael
5.2 years ago maryke.wijma • 0
0
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5
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4.9k
views
clusterProfiler: exclude pathways and add gene names to cnetplot
clusterprofiler pathway analysis pathways
updated 10 months ago by • 0 • written 5.3 years ago by ▴ 20
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0
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783
views
SPIA function error in ToPASeq
ToPASeq SPIA pathway analysis R
5.5 years ago fawazfebin ▴ 60
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3
replies
988
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Collapsing transcript counts into pathways / gene lists with DESeq2
deseq2 pathway analysis tximport
updated 5.5 years ago by 40k • written 5.5 years ago by • 0
0
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0
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1.1k
views
miR2Pathway Finite Observations
pathway analysis mirna parallel
5.5 years ago genomic8328 ▴ 10
1
vote
0
replies
1.7k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
5.5 years ago digrigor ▴ 10
0
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3
replies
1.1k
views
kegga error from edgeR
edger r bioconductor pathway analysis kegg
updated 5.6 years ago by 48k • written 5.6 years ago by ▴ 110
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0
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1.0k
views
pathview and gage server connection issue
pathview gage pathway analysis kegg visualization
5.6 years ago Luo Weijun ★ 1.6k
0
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1
reply
880
views
How to identify Disease biomarkers " DNA sequences as biomarkers "
dnaseq pathway analysis protein biomarkers
5.6 years ago emadelhewihy • 0
0
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1
reply
1.4k
views
PANTHER.db- external pointer error
goseq pantherdb pathway analysis gene ontology
updated 5.8 years ago by 63k • written 5.8 years ago by ▴ 10
3
votes
2
replies
3.8k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 5.9 years ago by ★ 1.2k • written 5.9 years ago by ▴ 10
1
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3
replies
1.2k
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 5.9 years ago by ▴ 720 • written 5.9 years ago by • 0
2
votes
11
replies
3.9k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
6.2 years ago Luo Weijun ★ 1.6k
0
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0
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1.0k
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Problem about functional annotation network of WGCNA modules (modified)
wgcna network analysis pathway analysis
6.2 years ago panagiotis.mokos ▴ 40
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0
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893
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SPIA Package : Activated and Inhibited
SPIA R pathway analysis
6.2 years ago khhgng • 0
0
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0
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1.2k
views
News: Pathview Web server published in NAR
pathway analysis visualization data integration omics pathview News
6.4 years ago Luo Weijun ★ 1.6k
1
vote
1
reply
960
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DESeq2 function in interpreting the differential expression results in terms of higher order biological processes or molecular pathways
pathway analysis deseq2
updated 6.4 years ago by 40k • written 6.4 years ago by • 0
1
vote
1
reply
1.0k
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 6.5 years ago by ★ 3.7k • written 6.5 years ago by • 0
0
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3
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2.0k
views
topGO - treating up- and down-regulated genes separately
topGO GSEA pathway analysis
updated 6.5 years ago by ▴ 720 • written 6.5 years ago by • 0
4
votes
7
replies
1.7k
views
Issues uploading database for metabolomic data analysis with Pathway Activity Profiling - PAPi
papi metabolomics pathway analysis
updated 6.6 years ago by ▴ 10 • written 7.4 years ago by ▴ 10
1
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4
replies
1.2k
views
Indirect path in KEGG, activation or inhibition?
bioconductor graphite kegg pathway analysis
updated 6.6 years ago by ▴ 100 • written 6.6 years ago by • 0
1
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2
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1.2k
views
KEGG data error?
bioconductor graphite pathway analysis
updated 6.6 years ago by ▴ 100 • written 6.6 years ago by • 0
0
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4
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1.2k
views
DESeq2 normalization prior to identification of highly-expressed functional categories
deseq2 pathway analysis order normalization
updated 6.7 years ago by 40k • written 6.7 years ago by • 0
0
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0
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1.1k
views
gene over-representation analysis with custom background
pathway analysis over-representation analysis DAVID pantherDB consensuspathDB
6.8 years ago smt8n • 0
2
votes
2
replies
2.8k
views
Why Pathview shows just red color (up-regulated genes) on a pathway?
Pathview pathway analysis differential gene expression
updated 7.2 years ago by ★ 1.6k • written 7.2 years ago by ▴ 10
1
vote
2
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1.6k
views
Please help with pathway analysis using Pathview
pathview pathway analysis
updated 7.2 years ago by ★ 1.6k • written 7.2 years ago by ▴ 10
0
votes
3
replies
3.3k
views
Gene ontology and pathway analysis in R - replicate ToppGene features; best strategy for getting annotations?
topgo biomart gene ontology goexpress pathway analysis
updated 7.3 years ago by ▴ 320 • written 7.3 years ago by ▴ 120
1
vote
3
replies
1.3k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
7.6 years ago serpalma.v ▴ 60
2
votes
3
replies
1.7k
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 7.6 years ago by 63k • written 7.6 years ago by ▴ 60
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0
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1.5k
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Pathview Web Server: user friendly pathway visualization and data integration
pathview pathway analysis visualization web server omics data
7.7 years ago Weijun Luo • 0
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0
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1.1k
views
Error with R package RontoTools regarding administrator issues downloading updated KEGG data
ROntoTools Rstudio bioconductor administratorIssues pathway analysis
8.0 years ago svlachavas ▴ 810
1
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2
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2.2k
views
(Gene-set)Pathway analysis based on network/pathway topology in R
SPIA functional enrichment pathway topology pathway analysis bioconductor
8.2 years ago svlachavas ▴ 810
2
votes
2
replies
1.5k
views
Output from pathview does not seem to match input
pathview gage pathway analysis
updated 8.2 years ago by ★ 1.6k • written 8.2 years ago by • 0
8
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4
replies
1.5k
views
NaN results on some pathways in CAMERA
camera edger pathway analysis
updated 8.3 years ago by 48k • written 8.3 years ago by 7.8k
0
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4
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1.4k
views
Argument gene.data for the correct implementation of fuction pathview of the pathview package
mroast limma pathview pathway analysis
updated 8.5 years ago by ★ 1.6k • written 8.5 years ago by ▴ 810
2
votes
6
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1.4k
views
Appropriate use of the function mroast to find KEGG pathways for differential expression
mroast limma pathway analysis differential gene expression affymetrix
8.5 years ago svlachavas ▴ 810
0
votes
1
reply
1.8k
views
SPIA error - names of de are not in reference array
SPIA named vectors pathway analysis
updated 13 months ago by • 0 • written 8.9 years ago by • 0
44 results • Page 1 of 1
Recent ...
Replies
Answer: ukb Chromosomal position information was converted into SNPS by James W. MacDonald 63k
In my work, we almost always convert RSIDs to chr:pos because the former is ambiguous and changing whereas the latter is not. Which is like…
Comment: T.fit function of maSigPro returns error message by hanna.g • 0
Addition to the issue above: the T.fit function works only when choosing the step.method = "forward", for whatever reason. Maybe this clue …
Answer: Deseq2, enrichGO and ensembl ID by James W. MacDonald 63k
1. There isn't a keytype alternative. You need the gene IDs. 2. Convert the `rownames` of your 'se' object, or the `rownames` of your `D…
Comment: Doubts regarding Pathview by loyedbend2811 • 0
I thoroughly enjoyed reading your essay, and it was quite beneficial to me. Please join me in [monopoly online][1] if you have the time. …
Comment: ukb Chromosomal position information was converted into SNPS by wenbo • 0
Hi, I downloaded uk biobank data, but I don't know how to use R to convert chromosome position information to rs
Votes
Answer: MDS plot edgeR
A: legend with gradient in ComplexHeatmap
Comment: comparing contrasts in edger/lima using makeContrasts function
Answer: comparing contrasts in edger/lima using makeContrasts function
Answer: Differential expression analysis with only FPKM matrix available from total newb
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