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Showing top results for tag: KEGG • reset
3
votes
5
replies
442
views
Gene set enrichment analysis gives a lot of "significant pathways"
KEGG GESA Hallmarks
6 days ago by Bine ▴ 70
0
votes
0
replies
101
views
EnrichKEGG issue
KEGG overrepresentation enrichment
14 days ago by am29 ▴ 40
0
votes
2
replies
233
views
KEGG MAPPER Reconstruct
KEGG MAPPER
updated 29 days ago by 3.8k • written 29 days ago by • 0
0
votes
0
replies
161
views
Confusing Pathway Analysis Results from DAVID
DAVID Reactome KEGG
4 weeks ago by saamhasan55 ▴ 10
5
votes
3
replies
489
views
blast against Gene Ontology (GO), KEGG, and EuKaryotic Orthologous Group (KOG) databases
KEGG KOG blast GO
updated 8 weeks ago by ★ 28k • written 8 weeks ago by ▴ 50
1
vote
2
replies
1.4k
views
pathview - cannot open URL : HTTP status was '403 Forbidden'
R kegg pathview
updated 10 weeks ago by ▴ 50 • written 2.3 years ago by ▴ 10
0
votes
0
replies
217
views
Workflow for functional analysis of differential gene core modules: KEGG, GSEA, and GO enrichment
gsea ppi-network enrichment-analysis kegg
3 months ago by mizzika • 0
0
votes
1
reply
829
views
Enrichment analysis guide for msu7 rice genome
transcriptome KEGG MSU7 rice GOenrichment
updated 3 months ago by • 0 • written 14 months ago by • 0
0
votes
5
replies
505
views
Pathway analysis for DGEList
KEGG Pathway_analysis GO gene_expression DGEList
updated 3 months ago by ★ 2.1k • written 3 months ago by ▴ 20
0
votes
0
replies
190
views
KEGG pathways analysis (ko and map IDs)
ko kegg pathway map
updated 4 months ago by 146k • written 4 months ago by ▴ 10
0
votes
0
replies
279
views
R code for KEGG pathways output
KEGGREST dplyr KEGG R
5 months ago by doramora ▴ 10
0
votes
0
replies
213
views
KEGG pathway enrichment analysis in Zea mays with R
KEGG Zea-mays R
updated 5 months ago by 44k • written 5 months ago by • 0
0
votes
0
replies
204
views
Kegg Pathways to Circos
Genomics KEGG Circos
5 months ago by dlera.lozano ▴ 10
0
votes
0
replies
258
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition kegg module database genomics
5 months ago by O.rka ▴ 740
1
vote
1
reply
334
views
API kegg - IndexError: list index out of range
kegg API
updated 5 months ago by ▴ 20 • written 5 months ago by • 0
2
votes
7
replies
1.3k
views
KEGG analysis in R
KEGG clusterProfiler Zea-mays
updated 5 months ago by • 0 • written 6 months ago by ▴ 130
2
votes
2
replies
703
views
GSEA on non-model organisms: How to handle duplicated KEGG KO
KEGG GSEA clusterProfiler GhostKOALA
updated 6 months ago by ▴ 980 • written 6 months ago by • 0
0
votes
0
replies
196
views
How to check if a few pathways have relationship?
MSigdb REACTOME KEGG
7 months ago by Chris ▴ 340
0
votes
0
replies
234
views
MG-RAST KEGG KO Search
mg-rast kegg metagenomics ko
7 months ago by Jeremy ▴ 930
0
votes
5
replies
683
views
Same NCBI IDs for different Ensembl IDs / Multiple NCBI IDs for an Ensembl ID
KEGG ENTREZ ENSEMBL
7 months ago by Maxwell ▴ 20
0
votes
0
replies
200
views
Help plotting enrichment results - kegg terms
Enrichment-analysis KEGG
updated 8 months ago by 44k • written 8 months ago by • 0
0
votes
0
replies
305
views
Enzyme in Pathview
r metabolomic kegg pathview
updated 8 months ago by 164k • written 8 months ago by • 0
2
votes
6
replies
946
views
GO and KEGG
GO bulk-RNA-seq Rstudio KEGG
updated 8 months ago by ★ 1.8k • written 8 months ago by • 0
0
votes
0
replies
266
views
KEGG orthology ID to E. coli gene symbol
symbol KEGG convert
9 months ago by sooni ▴ 20
0
votes
0
replies
295
views
Pathview modifies LFC genes. Is this normal?
gage pathview KEGG R
9 months ago by Alex • 0
0
votes
0
replies
278
views
Gold Standard Gene Regulatory Network Data for Human Cell Cycle
pathway kegg
updated 9 months ago by 44k • written 9 months ago by • 0
1
vote
10
replies
1.3k
views
How to obtain the gene set of KEGG module
R gene-set KEGG
10 months ago by xingyu ▴ 10
0
votes
1
reply
567
views
Enrichment dotplot color
KEGG R GO Enrichment dotplot
updated 10 months ago by 13k • written 10 months ago by • 0
1
vote
3
replies
713
views
GO, KEGG, GSEA analysis with ~5 DEGs
GO KEGG
updated 10 months ago by 101k • written 10 months ago by ▴ 20
0
votes
0
replies
349
views
extracting Uniprot IDs for Kegg pathways
mapping uniprot R kegg clusterprofiler
11 months ago by Assa Yeroslaviz ★ 1.9k
4
votes
2
replies
599
views
KEGG DATABASE
DATABASE KEGG
updated 11 months ago by ★ 1.8k • written 11 months ago by • 0
0
votes
0
replies
414
views
How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?
biomart kegg deseq2
11 months ago by bioinfo ▴ 150
0
votes
0
replies
304
views
KEGG module and abundance of its KEGG Orthologs for functioning
function kegg abundance
11 months ago by Jonathan Yoou ▴ 60
0
votes
0
replies
322
views
Pathview Enzyme Code to Gene Symbol Conversion
Pathview KEGG
11 months ago by B.N. ▴ 10
0
votes
0
replies
492
views
Trouble Adding Log Fold Changes to KEGG Pathway Visualization
KEGG RStudio
updated 11 months ago by 44k • written 11 months ago by • 0
4
votes
4
replies
1.1k
views
Combining GO and KEGG enrichments
Cytoscape KEGG network RNASeq GO
11 months ago by David R ▴ 20
0
votes
5
replies
1.0k
views
R Kegg Need help ASAP
KEGG RStudio
updated 12 months ago by 44k • written 12 months ago by • 0
0
votes
0
replies
380
views
RAP.ID to KEGG ID converter
RAP.ID KEGG RStudio
updated 12 months ago by 44k • written 12 months ago by • 0
0
votes
2
replies
786
views
To draw a heatmap displaying DEGs associated with a specific KEGG pathway.
heatmap KEGG DEG
updated 12 months ago by ▴ 70 • written 12 months ago by • 0
0
votes
0
replies
300
views
KEGG ribosomal gene found in metatranscriptome despite removing rRNA sequences
rRNA KEGG metatranscriptomics
12 months ago by kmat • 0
1
vote
2
replies
998
views
KEGG Pathway analysis for non-model organism using goseq
non-model-organism KEGG DEG
12 months ago by analyst ▴ 50
0
votes
0
replies
404
views
Data for pathview() (KEGG Pathway Map) after EdgeR
EdgeR LogFC pathview KEGG
13 months ago by Ann ▴ 40
5
votes
3
replies
1.5k
views
interpreting results from pathway analysis
RNA-seq kegg clusterprofiler GSEA pathway-analysis
updated 14 months ago by 44k • written 15 months ago by ▴ 40
0
votes
1
reply
713
views
Gene set enrichment analysis / Kegg analysis
kegg DGE RNAseq GSEA DESeq2
updated 14 months ago by ▴ 110 • written 14 months ago by • 0
0
votes
4
replies
804
views
KEGG adnotation
vizualization hordeum biologicalprocess KEGG
updated 14 months ago by ▴ 10 • written 15 months ago by ▴ 10
7
votes
6
replies
4.0k
views
7 follow
KEGG pathway maps
KEGG RNA-Seq
updated 15 months ago by ▴ 360 • written 8.0 years ago by ▴ 140
2
votes
2
replies
3.3k
views
From Kegg - Kaas to MetaCyc
kegg metacyc rna-seq
updated 15 months ago by ▴ 10 • written 10.6 years ago by ▴ 20
0
votes
0
replies
304
views
Extract KEGG pathway hierarchy
kegg hierarchy api
updated 15 months ago by 44k • written 15 months ago by • 0
0
votes
0
replies
424
views
What criteria are used to determine significant HMMER hits?
kegg protein kofamscan annotation metagenomics
15 months ago by O.rka ▴ 740
1
vote
2
replies
644
views
Downstream analysis of DEG for non-model organisms.
Axolotl KEGG GO GSEA
15 months ago by georgii.vdovin • 0
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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The choice of test depends on the types of variables involved and the hypothesis you have. But most importantly on the question you want am…
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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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any idea, how can I display the labels Pre and POst on the top of the heatmap? I am looking at complexheatmap package as to how they displa…
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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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