Showing : pathway analysis • reset
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Pathway analysis of bacterial RNA-seq data
annotation rna-seq pathway analysis
4.1 years ago microPhD • 0
0
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0
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673
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Pathviews for DE list of genes
pathviews RNAseq Pathway analysis
updated 5.1 years ago by 42k • written 5.1 years ago by • 0
5
votes
7
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9.2k
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Comparison between two different group's pathway analysis results
gage DESeq2 pathway analysis
updated 5.2 years ago by ▴ 280 • written 5.2 years ago by ▴ 10
5
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4
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1.9k
views
Function kegga not working for species other than the conventional ones - Pathways do not overlap with universe
kegga limma pathway analysis kegg
updated 5.5 years ago by 51k • written 5.5 years ago by ▴ 60
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816
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master gene list for pathway analysis
pathway analysis sigpathway Genesets_EntrezGeneIDs.RData
6.1 years ago maria • 0
1
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5
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3.3k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 3.3 years ago by • 0 • written 6.3 years ago by ▴ 40
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1
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1.1k
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
6.3 years ago ረ • 0
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0
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1.3k
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'names' attribute must be the same length as the vector - PAPi problems
PAPi metabolomics pathway analysis raphael
6.3 years ago maryke.wijma • 0
0
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5
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6.5k
views
clusterProfiler: exclude pathways and add gene names to cnetplot
clusterprofiler pathway analysis pathways
updated 2.0 years ago by • 0 • written 6.5 years ago by ▴ 20
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0
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1.1k
views
SPIA function error in ToPASeq
ToPASeq SPIA pathway analysis R
6.6 years ago fawazfebin ▴ 60
0
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3
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1.5k
views
Collapsing transcript counts into pathways / gene lists with DESeq2
deseq2 pathway analysis tximport
updated 6.6 years ago by 42k • written 6.6 years ago by • 0
0
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0
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1.4k
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miR2Pathway Finite Observations
pathway analysis mirna parallel
6.7 years ago genomic8328 ▴ 10
1
vote
0
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2.4k
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topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
6.7 years ago digrigor ▴ 10
0
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3
replies
1.6k
views
kegga error from edgeR
edger r bioconductor pathway analysis kegg
updated 6.7 years ago by 51k • written 6.7 years ago by ▴ 120
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0
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1.4k
views
pathview and gage server connection issue
pathview gage pathway analysis kegg visualization
6.8 years ago Luo Weijun ★ 1.6k
0
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1
reply
1.2k
views
How to identify Disease biomarkers " DNA sequences as biomarkers "
dnaseq pathway analysis protein biomarkers
6.8 years ago emadelhewihy • 0
0
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1
reply
1.8k
views
PANTHER.db- external pointer error
goseq pantherdb pathway analysis gene ontology
updated 6.9 years ago by 67k • written 6.9 years ago by ▴ 10
3
votes
2
replies
5.8k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 7.0 years ago by ★ 1.2k • written 7.0 years ago by ▴ 10
1
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3
replies
1.6k
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 7.0 years ago by ▴ 760 • written 7.0 years ago by • 0
2
votes
11
replies
5.1k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
7.3 years ago Luo Weijun ★ 1.6k
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0
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1.3k
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Problem about functional annotation network of WGCNA modules (modified)
wgcna network analysis pathway analysis
7.4 years ago panagiotis.mokos ▴ 40
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0
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1.2k
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SPIA Package : Activated and Inhibited
SPIA R pathway analysis
7.4 years ago khhgng • 0
0
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0
replies
1.6k
views
News: Pathview Web server published in NAR
pathway analysis visualization data integration omics pathview News
7.5 years ago Luo Weijun ★ 1.6k
1
vote
1
reply
1.2k
views
DESeq2 function in interpreting the differential expression results in terms of higher order biological processes or molecular pathways
pathway analysis deseq2
updated 7.5 years ago by 42k • written 7.6 years ago by • 0
1
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1
reply
1.4k
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 7.6 years ago by ★ 4.1k • written 7.6 years ago by • 0
0
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3
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2.6k
views
topGO - treating up- and down-regulated genes separately
topGO GSEA pathway analysis
updated 7.7 years ago by ▴ 760 • written 7.7 years ago by • 0
4
votes
7
replies
2.2k
views
Issues uploading database for metabolomic data analysis with Pathway Activity Profiling - PAPi
papi metabolomics pathway analysis
updated 7.7 years ago by ▴ 10 • written 8.6 years ago by ▴ 10
1
vote
4
replies
1.8k
views
Indirect path in KEGG, activation or inhibition?
bioconductor graphite kegg pathway analysis
updated 7.7 years ago by ▴ 100 • written 7.7 years ago by • 0
1
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2
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1.5k
views
KEGG data error?
bioconductor graphite pathway analysis
updated 7.7 years ago by ▴ 100 • written 7.7 years ago by • 0
0
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4
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1.5k
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DESeq2 normalization prior to identification of highly-expressed functional categories
deseq2 pathway analysis order normalization
updated 7.9 years ago by 42k • written 7.9 years ago by • 0
0
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0
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1.5k
views
gene over-representation analysis with custom background
pathway analysis over-representation analysis DAVID pantherDB consensuspathDB
7.9 years ago smt8n • 0
2
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2
replies
3.3k
views
Why Pathview shows just red color (up-regulated genes) on a pathway?
Pathview pathway analysis differential gene expression
updated 8.4 years ago by ★ 1.6k • written 8.4 years ago by ▴ 20
1
vote
2
replies
2.2k
views
Please help with pathway analysis using Pathview
pathview pathway analysis
updated 8.4 years ago by ★ 1.6k • written 8.4 years ago by ▴ 20
0
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3
replies
4.0k
views
Gene ontology and pathway analysis in R - replicate ToppGene features; best strategy for getting annotations?
topgo biomart gene ontology goexpress pathway analysis
updated 8.5 years ago by ▴ 350 • written 8.5 years ago by ▴ 130
1
vote
3
replies
1.8k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
8.7 years ago serpalma.v ▴ 60
2
votes
3
replies
2.1k
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 8.8 years ago by 67k • written 8.8 years ago by ▴ 60
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0
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1.8k
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Pathview Web Server: user friendly pathway visualization and data integration
pathview pathway analysis visualization web server omics data
8.9 years ago Weijun Luo • 0
0
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0
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1.4k
views
Error with R package RontoTools regarding administrator issues downloading updated KEGG data
ROntoTools Rstudio bioconductor administratorIssues pathway analysis
9.1 years ago svlachavas ▴ 830
1
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2
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2.6k
views
(Gene-set)Pathway analysis based on network/pathway topology in R
SPIA functional enrichment pathway topology pathway analysis bioconductor
9.3 years ago svlachavas ▴ 830
2
votes
2
replies
1.9k
views
Output from pathview does not seem to match input
pathview gage pathway analysis
updated 9.3 years ago by ★ 1.6k • written 9.3 years ago by • 0
8
votes
4
replies
1.9k
views
NaN results on some pathways in CAMERA
camera edger pathway analysis
updated 9.4 years ago by 51k • written 9.4 years ago by ★ 7.9k
0
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4
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1.7k
views
Argument gene.data for the correct implementation of fuction pathview of the pathview package
mroast limma pathview pathway analysis
updated 9.6 years ago by ★ 1.6k • written 9.6 years ago by ▴ 830
2
votes
6
replies
1.8k
views
Appropriate use of the function mroast to find KEGG pathways for differential expression
mroast limma pathway analysis differential gene expression affymetrix
9.6 years ago svlachavas ▴ 830
0
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1
reply
2.3k
views
SPIA error - names of de are not in reference array
SPIA named vectors pathway analysis
updated 2.3 years ago by • 0 • written 10.0 years ago by • 0
44 results • Page 1 of 1
Recent ...
Replies
Comment: Limma- Print-tip loess normalisation-printer layout information does not match M by dseauer • 0
Thank you so much for all of your help! I really appreciate it!
Comment: Limma- Print-tip loess normalisation-printer layout information does not match M by Gordon Smyth 51k
Thanks for extra info, but be careful that the Bioconductor support site requires code to be an markdown format. Copying code with prompts …
Comment: Limma- Print-tip loess normalisation-printer layout information does not match M by dseauer • 0
Thank you so much for your reply! I am sincerely sorry- of course I do not have multiple GAL files- just one- I meant gpr files! I am so so…
Comment: Is it possible to parallelise saveHDF5SummarizedExperiment by Stefano Mangiola ▴ 20
Thansk Herve', I will try. For reference this is the parallelization implementation of zellkonverter, to save anndata from SCE https://gi…
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore by Jason • 0
Any update on the resolution to this? I'm having the same issue with another species.
Votes
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: Handling biological replicates in DESeq2
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
biomaRt rnorvegicus_gene_ensembl not available anymore
A: Does edgeR need to specify reference group?
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