Showing : GOSemsim • reset
1
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12
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4.7k
views
Using GOsemsim to calculate semantic similarity between orthologus genes of two species
GOsemsim Gene ontology semantic similarity across species
updated 9.1 years ago by ★ 1.2k • written 9.1 years ago by ▴ 10
3
votes
12
replies
4.2k
views
Trouble installing GOSemSim
GOSemSim S4Vectors
6.8 years ago sergi.picart ▴ 20
0
votes
9
replies
3.7k
views
expired SQLiteConnection in GoSemSim package.
gene ontology GOSemsim
updated 10.5 years ago by ▴ 10 • written 10.8 years ago by • 0
0
votes
2
replies
3.4k
views
Can't install GO.db
GOexpress GO.db GOSemSim
3.2 years ago Chruut • 0
8
votes
5
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3.1k
views
Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not found
GOSemSim gosemsim gene ontology
updated 8.0 years ago by • 0 • written 8.0 years ago by ▴ 60
0
votes
1
reply
2.9k
views
GO vs GOALL in rrvgo and GOSemSim
rrvgo GOSemSim GO.db
5.6 years ago Jenny Drnevich ★ 2.0k
0
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3
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2.8k
views
using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 4.0 years ago by 53k • written 4.0 years ago by ▴ 90
0
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4
replies
2.7k
views
GOterm semantic similarity with non-reference organism
gosemsim go gene ontology
10.7 years ago cpcantalapiedra • 0
1
vote
1
reply
2.3k
views
How to get GOSemSim work on custom packages built with AnnotationForge
Guangchuang Yu GOSemSim AnnotationForge
updated 5.8 years ago by ★ 4.0k • written 5.8 years ago by • 0
1
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2
replies
2.3k
views
GOSemSim problem for yeast proteins
GOSemSim yeast
updated 11.0 years ago by ★ 1.2k • written 11.0 years ago by ▴ 10
2
votes
2
replies
2.2k
views
Error: could not find function "godata"
gosemsim
7.6 years ago anton.kratz ▴ 60
0
votes
5
replies
2.1k
views
Using mgeneSim with Ensembl ids
Ensembl GOsemsim GO semantic similarity
updated 9.4 years ago by ★ 1.2k • written 9.4 years ago by ▴ 10
0
votes
0
replies
2.1k
views
DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment genesetenrichment dose gosemsim
11.2 years ago Guangchuang Yu ★ 1.2k
0
votes
4
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2.1k
views
problem of GOSemSim R package operation geneSim()
gosemsim
9.7 years ago bnembarekmarwa • 0
0
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1
reply
1.9k
views
Normalization of specificity level (level of depth) of GO terms dataset
gosim gosemsim
updated 8.8 years ago by ▴ 760 • written 10.3 years ago by ▴ 10
0
votes
1
reply
1.9k
views
GOSemSim function, clusterSim throws expired SQLiteConnection error
GO GOSemSim GO GOSemSim
updated 12.2 years ago by ★ 1.2k • written 12.2 years ago by ★ 13k
1
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3
replies
1.8k
views
Meaning of NA in geneSim result using GOSemSim
GOSemSim Dnet
6.5 years ago helenlong1 • 0
0
votes
1
reply
1.8k
views
(pack: GOSemSim) NA semantic similarities between gene clusters
GO SemSim GOSemSim GO SemSim GOSemSim
updated 13.5 years ago by ★ 1.2k • written 13.5 years ago by ★ 13k
0
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2
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1.7k
views
(GOSemSim package) secondary GO terms generating NA values
gosemsim
updated 7.1 years ago by ★ 1.2k • written 7.2 years ago by • 0
1
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1
reply
1.7k
views
GOSemSim Package - mgeneSim() function / In is.na(go) : is.na() applied to non-(list or vector) of type 'NULL'
GOSemSim mgeneSim
updated 9.8 years ago by ★ 1.2k • written 9.8 years ago by • 0
0
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1
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1.6k
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 16.4 years ago by ★ 7.2k • written 16.4 years ago by ▴ 20
0
votes
1
reply
1.6k
views
GO similarity by GOSemSim
gosemsim similarity
7.6 years ago ahatashkar • 0
0
votes
1
reply
1.6k
views
GOSemSim: "godata" function can not run using self-made org.db.package.
GOSemSim makeOrgPackage godata
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
0
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0
replies
1.5k
views
GOSemSim - slow for BP terms
gosemsim go enrichment go semantic similarity
7.1 years ago nooshin ▴ 300
0
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1
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1.5k
views
is there an R library to compute semantic similarity in SNOMED ontology?
goSemSim snomed semantic similarity
updated 5.3 years ago by 6.7k • written 5.3 years ago by • 0
0
votes
0
replies
1.5k
views
GOSemSim mgeneSim GO.BP calculation time
GO GOSemSim GO GOSemSim
13.4 years ago Guangchuang Yu ★ 1.2k
0
votes
1
reply
1.5k
views
Gene similarity by GOSemSim
gosemsim mgenesim
7.1 years ago athirak1986 • 0
0
votes
1
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1.5k
views
GOSemSim comparison between species
Yeast GOSemSim Yeast GOSemSim
updated 13.6 years ago by ★ 8.2k • written 13.6 years ago by ▴ 10
0
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0
replies
1.2k
views
GOSemSim mgeneSim GO.BP calculation time
GO GOSemSim GO GOSemSim
13.4 years ago Guest User ★ 13k
0
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1
reply
1.2k
views
Using GoSemSim with other Ontologies
GOSemSim
updated 6.5 years ago by ▴ 760 • written 6.5 years ago by • 0
1
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1
reply
1.2k
views
GoSemSim - function mgeneSim() is resulting in similarity matrix without 1s on diagonal
GOSim GOSemSim
updated 3.0 years ago by ▴ 760 • written 3.0 years ago by ▴ 10
0
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0
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1.2k
views
using annotation data of an organism(eg. Oryza sativa) from AnnotationHub for mgoSim
AnnotationHubSoftware GOSemSim annotation
4.0 years ago Amandeep • 0
0
votes
1
reply
910
views
GOSemSim - mgeneSim weird output
GOSemSim similarity
updated 2.5 years ago by ▴ 760 • written 2.5 years ago by • 0
0
votes
1
reply
779
views
Help using reduceSimMatrix with a custom annotation
AnnotationHub GOSemSim rrvgo
updated 9 months ago by ▴ 80 • written 14 months ago by • 0
34 results • Page 1 of 1
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Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Confirming my understanding after executing the code provided: this is similar to a design formula of `~0+mouse+group+group:allele`, except…
Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
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A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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