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Showing top results for tag: pathways • reset
0
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2
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714
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Mapping Mouse RNAseq Marker Genes to Reactome Pathways
RNA-seq single-cell pathways reactome
updated 6 weeks ago by • 0 • written 11 months ago by ▴ 40
2
votes
4
replies
1000
views
Microbial pathway analysis tool or pipeline
pathways 16SrRNA microbiome
9 weeks ago by seda ▴ 20
0
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0
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226
views
How to Obtain a GMT File for Pathway Enrichment Analysis in Gallus gallus Metabolomics Data?
metabolomics gsea pathways gmt
3 months ago by DareDevil ★ 4.3k
0
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2
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523
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gProfiler vs Panther_go in overrepresentation pathways R analysis
pathways Reactome Panther Overrepresentation gProfiler
updated 4 months ago by ▴ 20 • written 5 months ago by • 0
0
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1
reply
388
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Annotating Pathways in a network
Pathways Cytoscape Network
updated 4 months ago by ▴ 280 • written 4 months ago by ▴ 60
3
votes
1
reply
432
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Trouble understanding seemingly contradicting results of GSE analysis (contradicting enriched GO terms with similar negative NES scores)
GSEA pathways GO-terms
updated 6 months ago by 20k • written 6 months ago by ▴ 10
0
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2
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581
views
How to obtain Node/ Edge information from a Reactome Pathway
R API pathways reactome databases
updated 7 months ago by 146k • written 8 months ago by ▴ 150
0
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1
reply
494
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Database for immunological pathways
pathways immunology pathway database
updated 10 months ago by ★ 1.8k • written 10 months ago by ▴ 530
0
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0
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801
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Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
17 months ago by Coremine Medical ▴ 20
0
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0
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370
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Simulation of pathways in scRNA
scRNA simulation pathways
19 months ago by sp29 ▴ 50
0
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1
reply
454
views
Get pathways containing input genes; Reactome Database
ensembl pathways reactome
updated 2.0 years ago by ▴ 810 • written 2.0 years ago by • 0
0
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0
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337
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Naming conventions for kegg nodes with multiple genes
xml pathways kegg kgml
2.2 years ago by travis • 0
1
vote
2
replies
651
views
Match genes with the pathway they participate
genes pathways databases
updated 2.3 years ago by 21k • written 2.3 years ago by • 0
0
votes
5
replies
1.1k
views
Pathway Analysis using GAGE
gage RNA-seq pathwayanalysis pathways gagedata
updated 2.6 years ago by ★ 1.8k • written 2.6 years ago by ▴ 10
1
vote
1
reply
463
views
Are there other options for Visualization of Organism-Scale Metabolic Networks
pathways Visualization metabolic
updated 2.6 years ago by 55k • written 2.6 years ago by • 0
1
vote
1
reply
536
views
Deseq2 output to ActivePathways
DeSeq2 matrix ActivePathways pathways p-value
updated 2.6 years ago by ★ 2.0k • written 2.6 years ago by ▴ 40
1
vote
0
replies
378
views
How do I display overlap in signalling pathways?
Pathways Signalling analysis overlap Pathway Kinase data
2.8 years ago by Niko ▴ 10
0
votes
2
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907
views
Pathways visualization as network
cytoscape Pathways
updated 2.9 years ago by ▴ 10 • written 2.9 years ago by ▴ 190
0
votes
2
replies
806
views
Query Modules from KEGG
pathways kegg modules
2.9 years ago by Schmoho ▴ 10
2
votes
4
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2.6k
views
kegg IDs to pathways in R
R KEGG list pathways
3.0 years ago by sapuizait ▴ 10
2
votes
2
replies
1.1k
views
Tool: miRAnno—network-based functional microRNA annotation
pathways miRNA annotation microRNA
3.3 years ago by tomastokar ▴ 50
1
vote
4
replies
1.2k
views
guilt by association
pathways analyses R
3.3 years ago by pinheirofabiano ▴ 90
1
vote
2
replies
885
views
How to pick top 50 the most abundant pathways?
pathways abundant
3.3 years ago by arshad1292 ▴ 110
0
votes
0
replies
499
views
Genes in GO pathways
GO pathways
3.4 years ago by some1 ▴ 10
5
votes
7
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2.2k
views
How to find the functions of Reactome pathways?
Pathways reactome pathways DAVID
updated 3.4 years ago by ▴ 580 • written 6.4 years ago by ▴ 260
6
votes
8
replies
1.5k
views
Diseases related pathways
pathways wikipathway kegg reactome
updated 3.5 years ago by ▴ 580 • written 3.8 years ago by ▴ 80
3
votes
2
replies
6.3k
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
clustering pathways complexheatmap pheatmap
3.6 years ago by Ridha ▴ 130
3
votes
5
replies
4.4k
views
Could somebody suggest free pathway visualization tool for omics data from plants?
Vizualization Pathways RNA-Seq
updated 3.6 years ago by ▴ 440 • written 6.4 years ago by ▴ 340
0
votes
1
reply
603
views
DESeq2 for specific genes
deseq2 RNA-Seq R specific genes pathways
updated 3.7 years ago by 14k • written 3.7 years ago by ▴ 40
0
votes
2
replies
2.5k
views
What is KEGG BRITE ?
kegg pathways metabolism
updated 3.7 years ago by ★ 1.4k • written 4.6 years ago by ▴ 70
7
votes
3
replies
15k
views
Enrichment Score Interpretation
RNA-Seq R pathways gsea Enrichment
updated 10 weeks ago by ▴ 360 • written 3.7 years ago by ▴ 20
3
votes
4
replies
1.5k
views
Obtaining directionality of pathways
Pathways R Reactome Wikipathways Bioconductor
updated 23 months ago by ▴ 580 • written 3.9 years ago by ▴ 50
4
votes
2
replies
1.0k
views
How Can I plot this data in a heatmap?
R Heatmap Pathways Uniprot
updated 3.9 years ago by 35k • written 3.9 years ago by ▴ 110
3
votes
2
replies
1.8k
views
Extract Pathway Topological Graphs (With Metabolites) from Reactome and WikiPathways
pathways metabolomics graph topological analysis
updated 4.1 years ago by ▴ 10 • written 4.2 years ago by ▴ 50
2
votes
6
replies
2.3k
views
Pathways Analysis in R
pathways R DEG
updated 4.1 years ago by ▴ 580 • written 4.3 years ago by ▴ 20
0
votes
3
replies
1.3k
views
InterProScan for Plants
gene protein annotation pathways ontology
4.2 years ago by Ric ▴ 440
1
vote
1
reply
812
views
Pathways Analysis - pvalue
pathways analysis RNA-Seq p-values DEG
updated 4.2 years ago by ▴ 10 • written 4.2 years ago by ▴ 20
0
votes
0
replies
719
views
Repository of pathways or hallmark gene sets expressed by each cell line
cell lines pathways expression
4.2 years ago by 9606 ▴ 330
0
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1
reply
1.3k
views
How to make a Pathway enrichment Heatmap with padjusted values?
RNA-Seq r pathways heatmap
updated 4.3 years ago by 13k • written 4.3 years ago by ▴ 130
2
votes
4
replies
1.1k
views
Pathway and gene analysis based on GWAS results
SNP pathways GWAS
updated 4.3 years ago by ★ 4.8k • written 4.3 years ago by ▴ 100
28
votes
17
replies
23k
views
12 follow
Dotplot for filtered pathways result
pathways ggplot2 clusterProfiler r dotplot
2.9 years ago by Leite ★ 1.3k
6
votes
5
replies
2.6k
views
Cell type pathway ScRNAseq
RNAseq Pathways
updated 4.4 years ago by ★ 18k • written 4.4 years ago by ★ 1.2k
1
vote
2
replies
1.3k
views
Pathways Network Analysis Cytoscape
network RNA-Seq pathways cytoscape
updated 4.4 years ago by ▴ 620 • written 4.4 years ago by ▴ 810
1
vote
1
reply
1.8k
views
Pathway/Gene set z-score from log2FC
RNA-Seq pathways DE genes Enrichment analysis
updated 4.4 years ago by ▴ 790 • written 4.4 years ago by ▴ 120
2
votes
6
replies
2.5k
views
Drawing KEGG-type metabolic pathways
next-gen kegg pathways metabolic Drawing
4.4 years ago by zion22 ▴ 70
0
votes
0
replies
1.2k
views
Selecting specific pathways for cneplot.
clusterprofiler R enrichKEGG pathways
4.5 years ago by AP ▴ 20
1
vote
2
replies
798
views
How to find tryptophan metabolizing genes in bacterial genomes
genome alignment Genes Bacterial pathways
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 30
2
votes
4
replies
2.0k
views
What is the best way to analyze and enrich a list of DE genes from RNAseq?
R pathways enrichment RNA-Seq
updated 17 months ago by 44k • written 4.6 years ago by ▴ 130
11
votes
6
replies
9.2k
views
6 follow
KEGG pathways associated to a gene using BiomaRt
biomart kegg pathways R
updated 2.1 years ago by 44k • written 10.4 years ago by ▴ 190
0
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1
reply
1.1k
views
Interpretation of "less" and "greater" after running gage with `same.dir = TRUE`
RNA-Seq gage functional_analysis pathways kegg
4.7 years ago by tmms ▴ 10
50 results • Page 1 of 1
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Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by ATpoint 85k
> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect? You cannot. It's pe…
Comment: Comparing GSEA mutant data to wild type by conmul • 0
Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
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Thank you for your answer, it's very inspiring.
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I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
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The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applica…
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Did you perform blockwise module detection by any chance? Are your results object's contents sorted in blocks?
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The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
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What p-value do you mean? When and how did you calculate it?
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What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.
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One of the improvements that the using the `salmon` -> `tximport` -> `DESeq2` pipeline, over just a `counts`->`DESeq2` pipeline is the abil…
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