Showing : pathway analysis • reset
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Pathway analysis of bacterial RNA-seq data
annotation rna-seq pathway analysis
3.6 years ago microPhD • 0
0
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0
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568
views
Pathviews for DE list of genes
pathviews RNAseq Pathway analysis
updated 4.5 years ago by 41k • written 4.5 years ago by • 0
4
votes
7
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7.2k
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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
5
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4
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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
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0
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713
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master gene list for pathway analysis
pathway analysis sigpathway Genesets_EntrezGeneIDs.RData
5.6 years ago maria • 0
1
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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
0
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1
reply
983
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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
5.8 years ago ረ • 0
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0
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1.1k
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'names' attribute must be the same length as the vector - PAPi problems
PAPi metabolomics pathway analysis raphael
5.8 years ago maryke.wijma • 0
0
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5
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5.7k
views
clusterProfiler: exclude pathways and add gene names to cnetplot
clusterprofiler pathway analysis pathways
updated 18 months ago by • 0 • written 5.9 years ago by ▴ 20
0
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0
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923
views
SPIA function error in ToPASeq
ToPASeq SPIA pathway analysis R
6.1 years ago fawazfebin ▴ 60
0
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3
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1.3k
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Collapsing transcript counts into pathways / gene lists with DESeq2
deseq2 pathway analysis tximport
updated 6.1 years ago by 41k • written 6.1 years ago by • 0
0
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0
replies
1.2k
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miR2Pathway Finite Observations
pathway analysis mirna parallel
6.1 years ago genomic8328 ▴ 10
1
vote
0
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2.1k
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topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
6.1 years ago digrigor ▴ 10
0
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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
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0
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1.3k
views
pathview and gage server connection issue
pathview gage pathway analysis kegg visualization
6.2 years ago Luo Weijun ★ 1.6k
0
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1
reply
1.1k
views
How to identify Disease biomarkers " DNA sequences as biomarkers "
dnaseq pathway analysis protein biomarkers
6.2 years ago emadelhewihy • 0
0
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1
reply
1.6k
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
3
votes
2
replies
4.8k
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
1
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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
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
0
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0
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1.2k
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Problem about functional annotation network of WGCNA modules (modified)
wgcna network analysis pathway analysis
6.8 years ago panagiotis.mokos ▴ 40
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0
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1.0k
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SPIA Package : Activated and Inhibited
SPIA R pathway analysis
6.8 years ago khhgng • 0
0
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0
replies
1.4k
views
News: Pathview Web server published in NAR
pathway analysis visualization data integration omics pathview News
7.0 years ago Luo Weijun ★ 1.6k
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 41k • written 7.0 years ago by • 0
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 ★ 3.9k • written 7.1 years ago by • 0
0
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3
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2.3k
views
topGO - treating up- and down-regulated genes separately
topGO GSEA pathway analysis
updated 7.1 years ago by ▴ 730 • written 7.1 years ago by • 0
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 8.0 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
1
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2
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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
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4
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1.3k
views
DESeq2 normalization prior to identification of highly-expressed functional categories
deseq2 pathway analysis order normalization
updated 7.3 years ago by 41k • written 7.3 years ago by • 0
0
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0
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1.3k
views
gene over-representation analysis with custom background
pathway analysis over-representation analysis DAVID pantherDB consensuspathDB
7.4 years ago smt8n • 0
2
votes
2
replies
3.0k
views
Why Pathview shows just red color (up-regulated genes) on a pathway?
Pathview pathway analysis differential gene expression
updated 7.8 years ago by ★ 1.6k • written 7.8 years ago by ▴ 10
1
vote
2
replies
1.9k
views
Please help with pathway analysis using Pathview
pathview pathway analysis
updated 7.8 years ago by ★ 1.6k • written 7.8 years ago by ▴ 10
0
votes
3
replies
3.6k
views
Gene ontology and pathway analysis in R - replicate ToppGene features; best strategy for getting annotations?
topgo biomart gene ontology goexpress pathway analysis
updated 7.9 years ago by ▴ 350 • written 7.9 years ago by ▴ 120
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
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 8.2 years ago by 65k • written 8.2 years ago by ▴ 60
0
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0
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1.6k
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Pathview Web Server: user friendly pathway visualization and data integration
pathview pathway analysis visualization web server omics data
8.3 years ago Weijun Luo • 0
0
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0
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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
1
vote
2
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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
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
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
0
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4
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1.5k
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
2
votes
6
replies
1.6k
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
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
44 results • Page 1 of 1
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Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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