Showing : GOsemsim • reset
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174
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Help using reduceSimMatrix with a custom annotation
AnnotationHub GOSemSim rrvgo
12 weeks ago daccar98 • 0
0
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1
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626
views
GOSemSim - mgeneSim weird output
GOSemSim similarity
updated 18 months ago by ▴ 760 • written 18 months ago by • 0
1
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1
reply
912
views
GoSemSim - function mgeneSim() is resulting in similarity matrix without 1s on diagonal
GOSim GOSemSim
updated 23 months ago by ▴ 760 • written 24 months ago by ▴ 10
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2
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2.4k
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Can't install GO.db
GOexpress GO.db GOSemSim
2.2 years ago Chruut • 0
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0
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926
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using annotation data of an organism(eg. Oryza sativa) from AnnotationHub for mgoSim
AnnotationHubSoftware GOSemSim annotation
3.0 years ago Amandeep • 0
0
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3
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2.3k
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using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 3.0 years ago by 52k • written 3.0 years ago by ▴ 90
0
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1
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1.3k
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is there an R library to compute semantic similarity in SNOMED ontology?
goSemSim snomed semantic similarity
updated 4.3 years ago by 6.7k • written 4.3 years ago by • 0
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1
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1.3k
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GOSemSim: "godata" function can not run using self-made org.db.package.
GOSemSim makeOrgPackage godata
updated 4.6 years ago by 67k • written 4.6 years ago by • 0
0
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1
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2.2k
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GO vs GOALL in rrvgo and GOSemSim
rrvgo GOSemSim GO.db
4.7 years ago Jenny Drnevich ★ 2.0k
1
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1
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1.9k
views
How to get GOSemSim work on custom packages built with AnnotationForge
Guangchuang Yu GOSemSim AnnotationForge
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by • 0
1
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3
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1.4k
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Meaning of NA in geneSim result using GOSemSim
GOSemSim Dnet
5.5 years ago helenlong1 • 0
0
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1
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1.0k
views
Using GoSemSim with other Ontologies
GOSemSim
updated 5.6 years ago by ▴ 760 • written 5.6 years ago by • 0
3
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12
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3.2k
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Trouble installing GOSemSim
GOSemSim S4Vectors
5.9 years ago sergi.picart ▴ 20
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1
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1.2k
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Gene similarity by GOSemSim
gosemsim mgenesim
6.1 years ago athirak1986 • 0
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0
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1.2k
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GOSemSim - slow for BP terms
gosemsim go enrichment go semantic similarity
6.1 years ago nooshin ▴ 300
0
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2
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1.4k
views
(GOSemSim package) secondary GO terms generating NA values
gosemsim
updated 6.2 years ago by ★ 1.2k • written 6.2 years ago by • 0
2
votes
2
replies
2.0k
views
Error: could not find function "godata"
gosemsim
6.6 years ago anton.kratz ▴ 60
0
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1
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1.3k
views
GO similarity by GOSemSim
gosemsim similarity
6.6 years ago ahatashkar • 0
8
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5
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2.7k
views
Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not found
GOSemSim gosemsim gene ontology
updated 7.0 years ago by • 0 • written 7.0 years ago by ▴ 60
0
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1
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1.6k
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Normalization of specificity level (level of depth) of GO terms dataset
gosim gosemsim
updated 7.8 years ago by ▴ 760 • written 9.3 years ago by ▴ 10
1
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12
replies
3.9k
views
Using GOsemsim to calculate semantic similarity between orthologus genes of two species
GOsemsim Gene ontology semantic similarity across species
updated 8.1 years ago by ★ 1.2k • written 8.2 years ago by ▴ 10
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5
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1.8k
views
Using mgeneSim with Ensembl ids
Ensembl GOsemsim GO semantic similarity
updated 8.4 years ago by ★ 1.2k • written 8.4 years ago by ▴ 10
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4
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1.7k
views
problem of GOSemSim R package operation geneSim()
gosemsim
8.8 years ago bnembarekmarwa • 0
1
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1
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1.4k
views
GOSemSim Package - mgeneSim() function / In is.na(go) : is.na() applied to non-(list or vector) of type 'NULL'
GOSemSim mgeneSim
updated 8.8 years ago by ★ 1.2k • written 8.8 years ago by • 0
0
votes
9
replies
3.2k
views
expired SQLiteConnection in GoSemSim package.
gene ontology GOSemsim
updated 9.5 years ago by ▴ 10 • written 9.8 years ago by • 0
0
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4
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2.2k
views
GOterm semantic similarity with non-reference organism
gosemsim go gene ontology
9.8 years ago cpcantalapiedra • 0
1
vote
2
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2.0k
views
GOSemSim problem for yeast proteins
GOSemSim yeast
updated 10.0 years ago by ★ 1.2k • written 10.0 years ago by ▴ 10
0
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0
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1.9k
views
DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment genesetenrichment dose gosemsim
10.2 years ago Guangchuang Yu ★ 1.2k
0
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1
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1.6k
views
GOSemSim function, clusterSim throws expired SQLiteConnection error
GO GOSemSim GO GOSemSim
updated 11.2 years ago by ★ 1.2k • written 11.2 years ago by ★ 13k
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0
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1.4k
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GOSemSim mgeneSim GO.BP calculation time
GO GOSemSim GO GOSemSim
12.4 years ago Guangchuang Yu ★ 1.2k
0
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0
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1.1k
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GOSemSim mgeneSim GO.BP calculation time
GO GOSemSim GO GOSemSim
12.4 years ago Guest User ★ 13k
0
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1
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1.5k
views
(pack: GOSemSim) NA semantic similarities between gene clusters
GO SemSim GOSemSim GO SemSim GOSemSim
updated 12.5 years ago by ★ 1.2k • written 12.5 years ago by ★ 13k
0
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1
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1.3k
views
GOSemSim comparison between species
Yeast GOSemSim Yeast GOSemSim
updated 12.6 years ago by ★ 8.2k • written 12.7 years ago by ▴ 10
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1
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1.4k
views
Gene ID of yeast in GOSemSim and other GO related package may need update
Annotation GO Yeast biomaRt GOSemSim GOSim Annotation GO Yeast biomaRt GOSemSim GOSim
updated 15.4 years ago by ★ 7.2k • written 15.4 years ago by ▴ 20
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Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
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Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
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