Showing : GOSemsim • reset
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Help using reduceSimMatrix with a custom annotation
AnnotationHub GOSemSim rrvgo
4 days ago daccar98 • 0
0
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1
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584
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GOSemSim - mgeneSim weird output
GOSemSim similarity
updated 16 months ago by ▴ 760 • written 16 months ago by • 0
1
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1
reply
850
views
GoSemSim - function mgeneSim() is resulting in similarity matrix without 1s on diagonal
GOSim GOSemSim
updated 21 months ago by ▴ 760 • written 21 months ago by ▴ 10
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2
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2.1k
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Can't install GO.db
GOexpress GO.db GOSemSim
24 months ago Chruut • 0
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0
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872
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using annotation data of an organism(eg. Oryza sativa) from AnnotationHub for mgoSim
AnnotationHubSoftware GOSemSim annotation
2.8 years ago Amandeep • 0
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3
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2.1k
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using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 2.8 years ago by 51k • written 2.8 years ago by ▴ 90
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1
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1.2k
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is there an R library to compute semantic similarity in SNOMED ontology?
goSemSim snomed semantic similarity
updated 4.1 years ago by 6.7k • written 4.1 years ago by • 0
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1.2k
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GOSemSim: "godata" function can not run using self-made org.db.package.
GOSemSim makeOrgPackage godata
updated 4.3 years ago by 67k • written 4.3 years ago by • 0
0
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1
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2.0k
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GO vs GOALL in rrvgo and GOSemSim
rrvgo GOSemSim GO.db
4.4 years ago Jenny Drnevich ★ 2.0k
1
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1
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1.6k
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How to get GOSemSim work on custom packages built with AnnotationForge
Guangchuang Yu GOSemSim AnnotationForge
updated 4.6 years ago by ★ 4.0k • written 4.6 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
5.3 years ago helenlong1 • 0
0
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1
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960
views
Using GoSemSim with other Ontologies
GOSemSim
updated 5.3 years ago by ▴ 760 • written 5.3 years ago by • 0
3
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12
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3.0k
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Trouble installing GOSemSim
GOSemSim S4Vectors
5.6 years ago sergi.picart ▴ 20
0
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1
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1.2k
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Gene similarity by GOSemSim
gosemsim mgenesim
5.9 years ago athirak1986 • 0
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0
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1.1k
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GOSemSim - slow for BP terms
gosemsim go enrichment go semantic similarity
5.9 years ago nooshin ▴ 300
0
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2
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1.3k
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(GOSemSim package) secondary GO terms generating NA values
gosemsim
updated 5.9 years ago by ★ 1.2k • written 5.9 years ago by • 0
2
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2
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2.0k
views
Error: could not find function "godata"
gosemsim
6.4 years ago anton.kratz ▴ 60
0
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1
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1.3k
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GO similarity by GOSemSim
gosemsim similarity
6.4 years ago ahatashkar • 0
8
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5
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2.6k
views
Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not found
GOSemSim gosemsim gene ontology
updated 6.7 years ago by • 0 • written 6.8 years ago by ▴ 60
0
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1
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1.5k
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Normalization of specificity level (level of depth) of GO terms dataset
gosim gosemsim
updated 7.6 years ago by ▴ 760 • written 9.1 years ago by ▴ 10
1
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12
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3.8k
views
Using GOsemsim to calculate semantic similarity between orthologus genes of two species
GOsemsim Gene ontology semantic similarity across species
updated 7.9 years ago by ★ 1.2k • written 7.9 years ago by ▴ 10
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5
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1.7k
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Using mgeneSim with Ensembl ids
Ensembl GOsemsim GO semantic similarity
updated 8.2 years ago by ★ 1.2k • written 8.2 years ago by ▴ 10
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4
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1.6k
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problem of GOSemSim R package operation geneSim()
gosemsim
8.5 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 8.6 years ago by ★ 1.2k • written 8.6 years ago by • 0
0
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9
replies
3.1k
views
expired SQLiteConnection in GoSemSim package.
gene ontology GOSemsim
updated 9.3 years ago by ▴ 10 • written 9.6 years ago by • 0
0
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4
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2.1k
views
GOterm semantic similarity with non-reference organism
gosemsim go gene ontology
9.5 years ago cpcantalapiedra • 0
1
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2
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2.0k
views
GOSemSim problem for yeast proteins
GOSemSim yeast
updated 9.8 years ago by ★ 1.2k • written 9.8 years ago by ▴ 10
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0
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1.8k
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DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment genesetenrichment dose gosemsim
10.0 years ago Guangchuang Yu ★ 1.2k
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1
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1.6k
views
GOSemSim function, clusterSim throws expired SQLiteConnection error
GO GOSemSim GO GOSemSim
updated 11.0 years ago by ★ 1.2k • written 11.0 years ago by ★ 13k
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1.3k
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GOSemSim mgeneSim GO.BP calculation time
GO GOSemSim GO GOSemSim
12.2 years ago Guangchuang Yu ★ 1.2k
0
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0
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1.0k
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GOSemSim mgeneSim GO.BP calculation time
GO GOSemSim GO GOSemSim
12.2 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 12.3 years ago by ★ 1.2k • written 12.3 years ago by ★ 13k
0
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1
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1.2k
views
GOSemSim comparison between species
Yeast GOSemSim Yeast GOSemSim
updated 12.4 years ago by ★ 8.2k • written 12.4 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 15.2 years ago by ★ 7.2k • written 15.2 years ago by ▴ 20
34 results • Page 1 of 1
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Replies
Comment: Volcano plot has many values around zero by Michael Love 42k
It's positive over zero or nearly so.
Answer: Volcano plot has many values around zero by swbarnes2 ★ 1.4k
You've got genes with supposedly have a 32-fold difference, and the adjusted p-values are < 1x10-10? That seems odd.
Comment: Volcano plot has many values around zero by mjun • 0
Why this cluster close to 0 with low p value is so distinctive. Is this common? What does it mean and why? Thanks
Comment: Volcano plot has many values around zero by swbarnes2 ★ 1.4k
I don't think this is evidence that the dataset is invalid. It's evidence that your experiment is underpowered, and/or your experimental c…
Comment: Differential Expression Analysis with unbalanced batches without replication bet by Gordon Smyth 51k
Have you read the totalVI documentation?, which says: > **Important** > We do not recommend using totalVI denoised values in other differ…
Votes
Comment: Weird looking volcano plot
Volcano plot has many values around zero
A: Up/Down Regulated GeneList from edgeR and R
A: Up/Down Regulated GeneList from edgeR and R
A: Down/Up-regulated genes asymmetry in edgeR differential expression analysis
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