Showing : pathway analysis • reset
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Pathway analysis of bacterial RNA-seq data
annotation rna-seq pathway analysis
5.1 years ago microPhD • 0
0
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0
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832
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Pathviews for DE list of genes
pathviews RNAseq Pathway analysis
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
5
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7
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12k
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Comparison between two different group's pathway analysis results
gage DESeq2 pathway analysis
updated 6.2 years ago by ▴ 280 • written 6.2 years ago by ▴ 10
5
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4
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2.3k
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Function kegga not working for species other than the conventional ones - Pathways do not overlap with universe
kegga limma pathway analysis kegg
updated 6.5 years ago by 53k • written 6.5 years ago by ▴ 60
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1.0k
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master gene list for pathway analysis
pathway analysis sigpathway Genesets_EntrezGeneIDs.RData
7.0 years ago maria • 0
1
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5
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3.9k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 4.3 years ago by • 0 • written 7.2 years ago by ▴ 40
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1
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1.4k
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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
7.3 years ago ረ • 0
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0
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1.6k
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'names' attribute must be the same length as the vector - PAPi problems
PAPi metabolomics pathway analysis raphael
7.3 years ago maryke.wijma • 0
0
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5
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7.4k
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clusterProfiler: exclude pathways and add gene names to cnetplot
clusterprofiler pathway analysis pathways
updated 3.0 years ago by • 0 • written 7.4 years ago by ▴ 20
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0
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1.3k
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SPIA function error in ToPASeq
ToPASeq SPIA pathway analysis R
7.6 years ago fawazfebin ▴ 60
0
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3
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1.8k
views
Collapsing transcript counts into pathways / gene lists with DESeq2
deseq2 pathway analysis tximport
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
0
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0
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1.6k
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miR2Pathway Finite Observations
pathway analysis mirna parallel
7.6 years ago genomic8328 ▴ 10
1
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0
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2.7k
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topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
7.6 years ago digrigor ▴ 10
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3
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2.0k
views
kegga error from edgeR
edger r bioconductor pathway analysis kegg
updated 7.7 years ago by 53k • written 7.7 years ago by ▴ 120
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0
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1.6k
views
pathview and gage server connection issue
pathview gage pathway analysis kegg visualization
7.7 years ago Luo Weijun ★ 1.6k
0
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1
reply
1.4k
views
How to identify Disease biomarkers " DNA sequences as biomarkers "
dnaseq pathway analysis protein biomarkers
7.7 years ago emadelhewihy • 0
0
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1
reply
2.2k
views
PANTHER.db- external pointer error
goseq pantherdb pathway analysis gene ontology
updated 7.9 years ago by 68k • written 7.9 years ago by ▴ 10
3
votes
2
replies
7.1k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 7.9 years ago by ★ 1.2k • written 8.0 years ago by ▴ 10
1
vote
3
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2.0k
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 8.0 years ago by ▴ 760 • written 8.0 years ago by • 0
2
votes
11
replies
5.9k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
8.3 years ago • updated 8.2 years ago Luo Weijun ★ 1.6k
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0
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1.5k
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Problem about functional annotation network of WGCNA modules (modified)
wgcna network analysis pathway analysis
8.3 years ago panagiotis.mokos ▴ 40
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1.4k
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SPIA Package : Activated and Inhibited
SPIA R pathway analysis
8.3 years ago khhgng • 0
0
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0
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1.9k
views
News: Pathview Web server published in NAR
pathway analysis visualization data integration omics pathview News
8.5 years ago • updated 8.4 years ago Luo Weijun ★ 1.6k
1
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1
reply
1.3k
views
DESeq2 function in interpreting the differential expression results in terms of higher order biological processes or molecular pathways
pathway analysis deseq2
updated 8.5 years ago by 43k • written 8.5 years ago by • 0
1
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1
reply
1.6k
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 8.6 years ago by ★ 4.1k • written 8.6 years ago by • 0
0
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3
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3.1k
views
topGO - treating up- and down-regulated genes separately
topGO GSEA pathway analysis
updated 8.6 years ago by ▴ 760 • written 8.6 years ago by • 0
4
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7
replies
2.5k
views
Issues uploading database for metabolomic data analysis with Pathway Activity Profiling - PAPi
papi metabolomics pathway analysis
updated 8.6 years ago by ▴ 10 • written 9.5 years ago by ▴ 10
1
vote
4
replies
2.2k
views
Indirect path in KEGG, activation or inhibition?
bioconductor graphite kegg pathway analysis
updated 8.7 years ago by ▴ 100 • written 8.7 years ago by • 0
1
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2
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1.8k
views
KEGG data error?
bioconductor graphite pathway analysis
updated 8.7 years ago by ▴ 100 • written 8.7 years ago by • 0
0
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4
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1.9k
views
DESeq2 normalization prior to identification of highly-expressed functional categories
deseq2 pathway analysis order normalization
updated 8.8 years ago by 43k • written 8.8 years ago by • 0
0
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0
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1.9k
views
gene over-representation analysis with custom background
pathway analysis over-representation analysis DAVID pantherDB consensuspathDB
8.9 years ago smt8n • 0
2
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2
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3.7k
views
Why Pathview shows just red color (up-regulated genes) on a pathway?
Pathview pathway analysis differential gene expression
updated 9.3 years ago by ★ 1.6k • written 9.3 years ago by ▴ 20
1
vote
2
replies
2.6k
views
Please help with pathway analysis using Pathview
pathview pathway analysis
updated 9.3 years ago by ★ 1.6k • written 9.3 years ago by ▴ 20
0
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3
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4.6k
views
Gene ontology and pathway analysis in R - replicate ToppGene features; best strategy for getting annotations?
topgo biomart gene ontology goexpress pathway analysis
updated 9.4 years ago by ▴ 350 • written 9.4 years ago by ▴ 130
1
vote
3
replies
2.2k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
9.7 years ago serpalma.v ▴ 60
2
votes
3
replies
2.4k
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 9.7 years ago by 68k • written 9.7 years ago by ▴ 60
0
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0
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2.0k
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Pathview Web Server: user friendly pathway visualization and data integration
pathview pathway analysis visualization web server omics data
9.8 years ago Weijun Luo • 0
0
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0
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1.6k
views
Error with R package RontoTools regarding administrator issues downloading updated KEGG data
ROntoTools Rstudio bioconductor administratorIssues pathway analysis
10.1 years ago svlachavas ▴ 840
1
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2
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2.9k
views
(Gene-set)Pathway analysis based on network/pathway topology in R
SPIA functional enrichment pathway topology pathway analysis bioconductor
10.3 years ago svlachavas ▴ 840
2
votes
2
replies
2.2k
views
Output from pathview does not seem to match input
pathview gage pathway analysis
updated 10.3 years ago by ★ 1.6k • written 10.3 years ago by • 0
8
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4
replies
2.3k
views
NaN results on some pathways in CAMERA
camera edger pathway analysis
updated 10.4 years ago by 53k • written 10.4 years ago by ★ 7.9k
0
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4
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2.0k
views
Argument gene.data for the correct implementation of fuction pathview of the pathview package
mroast limma pathview pathway analysis
updated 10.6 years ago by ★ 1.6k • written 10.6 years ago by ▴ 840
2
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6
replies
2.2k
views
Appropriate use of the function mroast to find KEGG pathways for differential expression
mroast limma pathway analysis differential gene expression affymetrix
10.6 years ago svlachavas ▴ 840
0
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1
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2.5k
views
SPIA error - names of de are not in reference array
SPIA named vectors pathway analysis
updated 3.2 years ago by • 0 • written 11.0 years ago by • 0
44 results • Page 1 of 1
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Comment: Join BOC Sciences at Drug Discovery Chemistry by teamardigen • 0
Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
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DESeq2 for candidate gene analysis
Join BOC Sciences at Drug Discovery Chemistry
Drug datasets for RNA-seq
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
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