Showing : keggsoap • reset
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KEGGSOAP:: KEGGxmlns object not found
keggsoap keggrest
7.4 years ago doctor.dee005 • 0
1
vote
5
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2.8k
views
About the state of KEGG-related packages
KEGGSOAP KEGGgraph keggorthology clusterProfiler KEGGprofile PathNet KEGGSOAP KEGGgraph
updated 12.2 years ago by ★ 1.6k • written 12.3 years ago by ▴ 680
1
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16
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2.7k
views
error installing KEGGSOAP
KEGGSOAP KEGGSOAP
updated 12.8 years ago by 25k • written 12.8 years ago by ▴ 420
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0
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1.4k
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KEGGREST package is available in devel
KEGGSOAP KEGGREST KEGGSOAP KEGGREST
12.8 years ago Dan Tenenbaum ★ 8.2k
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1
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1.0k
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Problem in KEGGSOAP package
KEGGSOAP KEGGSOAP
updated 12.8 years ago by ★ 8.2k • written 12.8 years ago by ▴ 120
0
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2
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1.3k
views
KEGGSOAP: list.pathways(org) or alternative way
Pathways Organism KEGGSOAP Pathways Organism KEGGSOAP
updated 13.2 years ago by ★ 7.2k • written 13.2 years ago by ▴ 30
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5
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1.5k
views
KEGGSOAP
KEGGSOAP KEGGSOAP
updated 13.6 years ago by ▴ 20 • written 13.7 years ago by ▴ 110
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1
reply
1.6k
views
FrozenRMA how to
Microarray Network hgu133plus2 Biobase PROcess KEGGSOAP beadarray EBImage edgeR frma
updated 13.7 years ago by ▴ 830 • written 13.7 years ago by ▴ 20
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1.2k
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PostForm() with KEGG
GO Cancer KEGGSOAP GO Cancer KEGGSOAP
13.7 years ago Voke AO ▴ 760
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1.2k
views
Problem using KEGGSOAP: multiple genes per identity
Pathways KEGGSOAP Pathways KEGGSOAP
13.7 years ago January Weiner ▴ 240
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2
replies
1.7k
views
A bug in either KEGG or KEGGSOAP?
Pathways KEGGSOAP Pathways KEGGSOAP
updated 13.8 years ago by ★ 7.2k • written 13.8 years ago by ▴ 230
0
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1
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997
views
KEGGSOAP
KEGGSOAP KEGGSOAP
updated 13.8 years ago by ★ 7.2k • written 13.8 years ago by ▴ 110
0
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1
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1.5k
views
KEGGsoap: Space required after the Public Identifier
KEGGSOAP KEGGSOAP
updated 13.8 years ago by 25k • written 13.8 years ago by ▴ 70
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1
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1.0k
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KEGGSOAP incomplete list.pathways
Pathways KEGGSOAP Pathways KEGGSOAP
updated 13.9 years ago by ★ 7.2k • written 13.9 years ago by ★ 13k
0
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2
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1.3k
views
Problem installing KEGGSOAP
KEGGSOAP KEGGSOAP
updated 13.9 years ago by ★ 8.2k • written 14.0 years ago by ▴ 140
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0
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997
views
SSOAP functions
KEGGSOAP KEGGSOAP
14.5 years ago Michael Gormley ▴ 60
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2
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3.8k
views
GEOquery -> cannot open URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/ ....
KEGGSOAP GEOquery KEGGSOAP GEOquery
updated 14.7 years ago by 21k • written 14.7 years ago by ▴ 340
0
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1
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1.8k
views
KEGGSOAP, hgu95av2.db: limited functionality
Pathways hgu95av2 probe KEGGSOAP Pathways hgu95av2 probe KEGGSOAP
updated 15.7 years ago by ★ 7.2k • written 15.7 years ago by ▴ 70
0
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2
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1.3k
views
KEGGSOAP returning blank pages
Cancer KEGGSOAP Cancer KEGGSOAP
updated 16.2 years ago by ★ 7.2k • written 16.2 years ago by ★ 1.9k
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1.2k
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KEGGSOAP package
KEGGSOAP KEGGSOAP
16.2 years ago Glazko, Galina ▴ 350
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1.2k
views
KEGGSOAP package: I can't retrieve KEGG pathway diagrams
hgu133a KEGGSOAP hgu133a KEGGSOAP
16.3 years ago Paolo Sonego ▴ 140
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3
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1.7k
views
KEGGSOAP: problem with get.pathways.by.genes()
Pathways convert KEGGSOAP Pathways convert KEGGSOAP
updated 16.5 years ago by ▴ 400 • written 16.5 years ago by ▴ 30
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0
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961
views
KEGGSOAP install problem
Cancer KEGGSOAP Cancer KEGGSOAP
16.5 years ago Daniel Brewer ★ 1.9k
0
votes
4
replies
1.5k
views
KEGGSOAP problem
KEGGSOAP KEGGSOAP
updated 16.5 years ago by 6.7k • written 16.5 years ago by ▴ 350
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2
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1.7k
views
KEGGSOAP (installation?) problem
KEGGSOAP KEGGSOAP
updated 16.5 years ago by ★ 7.2k • written 16.5 years ago by ▴ 140
0
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3
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1.7k
views
building enzyme centric metabolic network
Network KEGGSOAP Network KEGGSOAP
updated 16.5 years ago by 25k • written 16.5 years ago by ▴ 270
0
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3
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1.7k
views
Retrieving KEGG pathway diagrams via KEGGSOAP
KEGGSOAP KEGGSOAP
updated 16.5 years ago by ▴ 140 • written 16.5 years ago by ▴ 120
0
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0
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1.2k
views
Visulising KEGG pathways using KEGGSOAP - example code
Pathways geneplotter KEGGSOAP biomaRt GEOquery Pathways geneplotter KEGGSOAP biomaRt
16.5 years ago michael watson IAH-C ★ 3.4k
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1
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1.0k
views
KEGG pathway IDs ,issing
Annotation Cancer KEGGSOAP Annotation Cancer KEGGSOAP
updated 16.5 years ago by ★ 7.2k • written 16.5 years ago by ★ 1.9k
0
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1
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1.3k
views
KEGGSOAP: color.pathway.by.objects
Pathways KEGGSOAP Pathways KEGGSOAP
updated 18.2 years ago by ★ 2.9k • written 18.2 years ago by ▴ 30
0
votes
3
replies
1.2k
views
libraries or commands to help with parsing or handling web based database queries
PROcess KEGGSOAP PROcess KEGGSOAP
updated 18.7 years ago by ★ 1.7k • written 18.7 years ago by ▴ 40
0
votes
7
replies
1.8k
views
KEGGSOAP
KEGGSOAP KEGGSOAP
updated 18.9 years ago by ▴ 870 • written 18.9 years ago by ★ 6.0k
0
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0
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995
views
KEGGSOAP Question: get.pathways.by.compounds
Pathways KEGGSOAP Pathways KEGGSOAP
18.9 years ago Nianhua Li ▴ 870
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0
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1.2k
views
KEGGSOAP questions: how to handle multiple annotations in R data frames, and why does a "for" loop only use one annotation.
Annotation KEGGSOAP Annotation KEGGSOAP
18.9 years ago ALAN SMITH ▴ 40
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2
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1.4k
views
help with KEGG or KEGGSOAP
KEGGSOAP KEGGSOAP
updated 18.9 years ago by ▴ 870 • written 19.0 years ago by ▴ 40
0
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0
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899
views
Inconsistent results returned from KEGG
KEGGSOAP KEGGSOAP
19.6 years ago michael watson IAH-C ★ 3.4k
0
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12
replies
2.9k
views
KEGGSOAP
KEGGSOAP KEGGSOAP
updated 19.6 years ago by ★ 7.4k • written 19.6 years ago by ▴ 30
0
votes
0
replies
1.2k
views
problem with get.genes.by.pathway
Biobase reposTools KEGGSOAP Biobase reposTools KEGGSOAP
20.1 years ago Kimpel, Mark W ▴ 890
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1
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1.5k
views
Bioconductor Install Problems
Rgraphviz KEGGSOAP Rgraphviz KEGGSOAP
updated 20.8 years ago by ★ 7.4k • written 20.8 years ago by ▴ 10
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0
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820
views
mark.pathway.by.objects return NULL
KEGGSOAP KEGGSOAP
20.8 years ago Yi-Xiong Sean Zhou ▴ 50
0
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0
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1.2k
views
KEGGSOAP - Error in xmlName(node[[1]]) : no applicable method for "xmlName"
KEGGSOAP KEGGSOAP
20.8 years ago michael watson IAH-C ★ 3.4k
0
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2
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1.1k
views
Problems installing KEGGSOAP
KEGGSOAP KEGGSOAP
20.8 years ago michael watson IAH-C ★ 3.4k
0
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2
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1.6k
views
pathway analysis package
RBGL KEGGSOAP RBGL KEGGSOAP
updated 20.9 years ago by 21k • written 20.9 years ago by ▴ 60
43 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
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
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…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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