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Showing :
pathways
•
reset
2
votes
2
replies
169
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
14 days ago • updated 13 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
mike Ad.
▴ 30
0
votes
0
replies
343
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
486
views
topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation
missMethyl
Pathways
12 months ago
Grace
• 0
0
votes
0
replies
434
views
Changing pathway names in pathway analysis
pathways
Pathways
15 months ago
Katharina
• 0
0
votes
0
replies
592
views
Job:
EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq
Transcriptomics
Pathways
Epigenetics
RNASeq
17 months ago
whduke
• 0
0
votes
0
replies
719
views
Pathway Analysis using GAGE
gage
RNASeq
gageData
Pathways
2.0 years ago
OST
• 0
1
vote
2
replies
812
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
SamGG
▴ 350 • written 3.1 years ago by
r.i.s.alnuwaysir
▴ 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
927
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
James W. MacDonald
65k • written 3.4 years ago by
ojong
• 0
2
votes
1
reply
2.1k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 3.8 years ago by
Robert Castelo
★ 3.3k • written 3.8 years ago by
igor
▴ 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
Martin Morgan
25k • written 4.0 years ago by
predeus
• 0
0
votes
4
replies
992
views
Fonction of genes/metabolites in a pathway?
gene
metabolite
functionnal annotation
pathways
updated 4.1 years ago by
Kevin Blighe
★ 3.9k • written 4.1 years ago by
emisecherre
• 0
0
votes
0
replies
773
views
plotting Signalling Pathways using SPIA
SPIA
functional-analysis
Pathways
KEGG
4.1 years ago
Assa Yeroslaviz
★ 1.5k
2
votes
2
replies
966
views
Help for Research Proposal
drug development
pathways
bioinformatics
updated 5.4 years ago by
Steve Lianoglou
★ 13k • written 5.4 years ago by
wajeehaejaz17
• 0
0
votes
0
replies
957
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
671
views
Interactive metabolic pathway
pathways
5.7 years ago
pritim2k6
• 0
0
votes
1
reply
983
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
767
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
yuhang
• 0 • written 5.9 years ago by
Mr.RB
▴ 20
2
votes
4
replies
2.2k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways
reactomepa
functional annotation
updated 5.9 years ago by
Guangchuang Yu
★ 1.2k • written 5.9 years ago by
martin.busch
• 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
983
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
atanas.kamburov
• 0 • written 10.6 years ago by
Luo Weijun
★ 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
Luo Weijun
★ 1.6k • written 7.0 years ago by
snishtala03
• 0
0
votes
1
reply
2.0k
views
Pathview: visualization of data
pathways
updated 7.1 years ago by
Luo Weijun
★ 1.6k • written 7.1 years ago by
svmichaela
• 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
Monther Alhamdoosh
▴ 40 • written 7.6 years ago by
yingchen
• 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
najib
• 0 • written 8.3 years ago by
Dani
▴ 20
2
votes
1
reply
1.1k
views
Problem with data not found using pathview package
pathways
updated 8.9 years ago by
James W. MacDonald
65k • written 9.0 years ago by
nurhafizah.nazari
• 0
8
votes
14
replies
3.8k
views
reactome.db is not updated?
genesetenrichment
pathways
reactome.db
updated 9.1 years ago by
willem.ligtenberg
▴ 150 • written 9.4 years ago by
Guangchuang Yu
★ 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
willem.ligtenberg
▴ 150 • written 9.5 years ago by
Johannes Rainer
★ 2.0k
0
votes
2
replies
1.7k
views
retrieve kegg pathway abundances from gage analysis
gage
pathways
kegg
updated 9.2 years ago by
Luo Weijun
★ 1.6k • written 9.2 years ago by
francesca.defilippis
▴ 100
0
votes
13
replies
5.8k
views
gage pathways enrichment analysis
gage
pathways
kegg
updated 9.4 years ago by
Luo Weijun
★ 1.6k • written 9.4 years ago by
francesca.defilippis
▴ 100
0
votes
2
replies
4.4k
views
Pathway enrichment in bacteria metagenomes
pathways
metagenomics
updated 9.4 years ago by
Luo Weijun
★ 1.6k • written 9.4 years ago by
francesca.defilippis
▴ 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
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Replies
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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