Showing : Pathways • reset
2
votes
2
replies
165
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
12 days ago • updated 11 days ago julia_mcdonough • 0
0
votes
11
replies
2.0k
views
globaltest question
Pathways probe affy Pathways probe affy
written 17.6 years ago by ▴ 30
0
votes
0
replies
341
views
Job: Postdoc for computational biology on cancer omics data analysis at Liang lab of Wistar Institute, Philadelphia, US
omics cancerdata Pathways
3 months ago omicsresearch • 0
0
votes
1
reply
484
views
topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation missMethyl Pathways
12 months ago Grace • 0
0
votes
0
replies
431
views
Changing pathway names in pathway analysis
pathways Pathways
15 months ago Katharina • 0
0
votes
0
replies
589
views
Job: EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq Transcriptomics Pathways Epigenetics RNASeq
17 months ago whduke • 0
0
votes
0
replies
715
views
Pathway Analysis using GAGE
gage RNASeq gageData Pathways
2.0 years ago OST • 0
1
vote
2
replies
809
views
Pathway analysis of RNAseq data using goseq package
Pathways goseq RNASeqData
2.1 years ago m.glymenaki • 0
0
votes
6
replies
3.7k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
2.7 years ago Bogdan ▴ 670
0
votes
4
replies
4.9k
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
R Pathways pheatmap limma
updated 3.1 years ago by ▴ 350 • written 3.1 years ago by ▴ 10
1
vote
1
reply
1.1k
views
News: SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
SBGNview pathways SBGNview.data pathview visualization
3.1 years ago Luo Weijun ★ 1.6k
2
votes
0
replies
923
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
3.2 years ago Ben ▴ 50
2
votes
2
replies
1.1k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 3.4 years ago by 65k • written 3.4 years ago by • 0
2
votes
1
reply
2.0k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 3.8 years ago by ★ 3.3k • written 3.8 years ago by ▴ 40
0
votes
1
reply
1.7k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 4.0 years ago by 25k • written 4.0 years ago by • 0
0
votes
4
replies
991
views
Fonction of genes/metabolites in a pathway?
gene metabolite functionnal annotation pathways
updated 4.1 years ago by ★ 3.9k • written 4.1 years ago by • 0
0
votes
0
replies
770
views
plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.1 years ago Assa Yeroslaviz ★ 1.5k
2
votes
2
replies
962
views
Help for Research Proposal
drug development pathways bioinformatics
updated 5.4 years ago by ★ 13k • written 5.4 years ago by • 0
0
votes
0
replies
954
views
Pathview input error: non-numeric variable in data frame
pathview kegg pathways package
5.6 years ago anc.informatics • 0
0
votes
0
replies
669
views
Interactive metabolic pathway
pathways
5.7 years ago pritim2k6 • 0
0
votes
1
reply
982
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
5.8 years ago ረ • 0
0
votes
0
replies
765
views
Could not find pathways in HSA gmt
pathways gmt
5.9 years ago flalix • 0
0
votes
5
replies
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
2
votes
4
replies
2.1k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 5.9 years ago by ★ 1.2k • written 5.9 years ago by • 0
0
votes
0
replies
1.0k
views
Pathview web - unable to map transcriptomic data
pathways high-throughput transcriptomics nonmodel species
6.0 years ago monteiro • 0
0
votes
0
replies
981
views
igraph PoTRA error
graph pathways igraph
6.1 years ago genomic8328 ▴ 10
2
votes
1
reply
1.9k
views
Pathview graph with multiple states/samples or time series
Pathways graph Pathways graph
updated 6.2 years ago by • 0 • written 10.5 years ago by ★ 1.6k
0
votes
0
replies
1.2k
views
Two questions about pathifier package
pathways statistics microarray
6.3 years ago arronar • 0
1
vote
0
replies
1.4k
views
Job: Bioinformatician/Computational Biologist - Dublin City, Ireland
bioinformatician job computational biology genomes pathways machine learning Job
6.5 years ago bulfin.triona ▴ 10
0
votes
1
reply
1.9k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R GSEA GAGE pathways
updated 7.0 years ago by ★ 1.6k • written 7.0 years ago by • 0
0
votes
1
reply
2.0k
views
Pathview: visualization of data
pathways
updated 7.1 years ago by ★ 1.6k • written 7.1 years ago by • 0
0
votes
0
replies
1.2k
views
Pathway analysis for diffrential express gene
pathways gage annotation gostats
7.2 years ago avinash gupta ▴ 130
0
votes
0
replies
1.3k
views
Job: PhD student positions in the areas of Bioinformatics, Computer Science and Biostatistics
bioinformatician job phd R pathways Job
7.4 years ago Frank Kramer ▴ 60
0
votes
6
replies
1.5k
views
Is reactome.db still updated?
reactome.db annotation pathways
7.5 years ago Guido Hooiveld ★ 3.9k
0
votes
4
replies
1.9k
views
EGSEA: how does the program generate the value for the up or down regulation of gene sets or pathways
pathways gsea egsea gage
updated 7.6 years ago by ▴ 40 • written 7.6 years ago by • 0
2
votes
0
replies
1.4k
views
Job: PhD student positions in the areas of Bioinformatics, Computer Science and Biostatistics
bioinformatician job job phd R pathways Job
7.6 years ago Frank Kramer ▴ 60
0
votes
2
replies
2.7k
views
WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
8.3 years ago hywel.williams • 0
2
votes
3
replies
4.8k
views
Pathview None of the genes or compounds mapped to the pathway
pathview pathways KEGG empty map
updated 2.8 years ago by • 0 • written 8.3 years ago by ▴ 20
2
votes
1
reply
1.1k
views
Problem with data not found using pathview package
pathways
updated 8.9 years ago by 65k • written 8.9 years ago by • 0
8
votes
14
replies
3.8k
views
reactome.db is not updated?
genesetenrichment pathways reactome.db
updated 9.1 years ago by ▴ 150 • written 9.4 years ago by ★ 1.2k
1
vote
15
replies
3.4k
views
reactome.db: reactome IDs not mapped to pathway names
annotation pathways
updated 9.1 years ago by ▴ 150 • written 9.5 years ago by ★ 2.0k
0
votes
2
replies
1.7k
views
retrieve kegg pathway abundances from gage analysis
gage pathways kegg
updated 9.1 years ago by ★ 1.6k • written 9.2 years ago by ▴ 100
0
votes
13
replies
5.8k
views
gage pathways enrichment analysis
gage pathways kegg
updated 9.4 years ago by ★ 1.6k • written 9.4 years ago by ▴ 100
0
votes
2
replies
4.4k
views
Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 9.4 years ago by ★ 1.6k • written 9.4 years ago by ▴ 100
0
votes
0
replies
2.3k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
9.6 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
1.7k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
9.6 years ago Guest User ★ 13k
0
votes
0
replies
1.5k
views
Error in keggPathwayGraphs when updateCache = TRUE
Pathways ROntoTools Pathways ROntoTools
9.7 years ago Guest User ★ 13k
0
votes
0
replies
1.3k
views
ISMB talks: Pathview for pathway-based data integration and visualization
Pathways Visualization pathview Pathways Visualization pathview
9.8 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
1.1k
views
ECCB 2014
Sequencing Pathways Sequencing Pathways
9.9 years ago Wolfgang Raffelsberger ▴ 60
0
votes
0
replies
1.4k
views
PostDoc opportunity
Pathways Network Pathways Network
9.9 years ago Guest User ★ 13k
50 results • Page 1 of 1
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
Awards • All
Supporter to Jonathan ▴ 10
Popular Question to Bine ▴ 40
Scholar to ATpoint ★ 4.0k
Popular Question to Gordon Smyth 50k
Popular Question to i.sudbery ▴ 40
Locations • All
Spain, 4 minutes ago
France, 8 minutes ago
United States, 12 minutes ago
United States, 19 minutes ago
United States, 19 minutes ago
Traffic: 767 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6