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goSemSim
•
reset
0
votes
0
replies
182
views
Help using reduceSimMatrix with a custom annotation
AnnotationHub
GOSemSim
rrvgo
3 months ago
daccar98
• 0
0
votes
1
reply
637
views
GOSemSim - mgeneSim weird output
GOSemSim
similarity
updated 19 months ago by
Lluís Revilla Sancho
▴ 760 • written 19 months ago by
Giovanni
• 0
1
vote
1
reply
922
views
GoSemSim - function mgeneSim() is resulting in similarity matrix without 1s on diagonal
GOSim
GOSemSim
updated 2.0 years ago by
Lluís Revilla Sancho
▴ 760 • written 2.0 years ago by
eliska.ochodkova
▴ 10
0
votes
2
replies
2.5k
views
Can't install GO.db
GOexpress
GO.db
GOSemSim
2.2 years ago
Chruut
• 0
0
votes
0
replies
935
views
using annotation data of an organism(eg. Oryza sativa) from AnnotationHub for mgoSim
AnnotationHubSoftware
GOSemSim
annotation
3.0 years ago
Amandeep
• 0
0
votes
3
replies
2.3k
views
using the goana function from edgeR
RNASeq
edgeR
GO
GOSemSim
updated 3.0 years ago by
Gordon Smyth
52k • written 3.0 years ago by
David R
▴ 90
0
votes
1
reply
1.3k
views
is there an R library to compute semantic similarity in SNOMED ontology?
goSemSim
snomed
semantic similarity
updated 4.4 years ago by
Vincent J. Carey, Jr.
6.7k • written 4.4 years ago by
izem.rima
• 0
0
votes
1
reply
1.3k
views
GOSemSim: "godata" function can not run using self-made org.db.package.
GOSemSim
makeOrgPackage
godata
updated 4.6 years ago by
James W. MacDonald
68k • written 4.6 years ago by
Wojeff
• 0
0
votes
1
reply
2.2k
views
GO vs GOALL in rrvgo and GOSemSim
rrvgo
GOSemSim
GO.db
4.7 years ago
Jenny Drnevich
★ 2.0k
1
vote
1
reply
1.9k
views
How to get GOSemSim work on custom packages built with AnnotationForge
Guangchuang Yu
GOSemSim
AnnotationForge
updated 4.8 years ago by
Kevin Blighe
★ 4.0k • written 4.8 years ago by
Cei
• 0
1
vote
3
replies
1.4k
views
Meaning of NA in geneSim result using GOSemSim
GOSemSim
Dnet
5.6 years ago
helenlong1
• 0
0
votes
1
reply
1.0k
views
Using GoSemSim with other Ontologies
GOSemSim
updated 5.6 years ago by
Lluís Revilla Sancho
▴ 760 • written 5.6 years ago by
helenlong1
• 0
3
votes
12
replies
3.2k
views
Trouble installing GOSemSim
GOSemSim
S4Vectors
5.9 years ago
sergi.picart
▴ 20
0
votes
1
reply
1.2k
views
Gene similarity by GOSemSim
gosemsim
mgenesim
6.1 years ago
athirak1986
• 0
0
votes
0
replies
1.2k
views
GOSemSim - slow for BP terms
gosemsim
go enrichment
go semantic similarity
6.2 years ago
nooshin
▴ 300
0
votes
2
replies
1.4k
views
(GOSemSim package) secondary GO terms generating NA values
gosemsim
updated 6.2 years ago by
Guangchuang Yu
★ 1.2k • written 6.2 years ago by
l.willianpacheco
• 0
2
votes
2
replies
2.0k
views
Error: could not find function "godata"
gosemsim
6.6 years ago
anton.kratz
▴ 60
0
votes
1
reply
1.4k
views
GO similarity by GOSemSim
gosemsim
similarity
6.7 years ago
ahatashkar
• 0
8
votes
5
replies
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
ellascottgm
• 0 • written 7.0 years ago by
anton.kratz
▴ 60
0
votes
1
reply
1.6k
views
Normalization of specificity level (level of depth) of GO terms dataset
gosim
gosemsim
updated 7.9 years ago by
Lluís Revilla Sancho
▴ 760 • written 9.4 years ago by
s.apocarpum
▴ 10
1
vote
12
replies
4.0k
views
Using GOsemsim to calculate semantic similarity between orthologus genes of two species
GOsemsim
Gene ontology
semantic similarity
across species
updated 8.2 years ago by
Guangchuang Yu
★ 1.2k • written 8.2 years ago by
saadmurtazakhan
▴ 10
0
votes
5
replies
1.8k
views
Using mgeneSim with Ensembl ids
Ensembl
GOsemsim
GO semantic similarity
updated 8.5 years ago by
Guangchuang Yu
★ 1.2k • written 8.5 years ago by
saadmurtazakhan
▴ 10
0
votes
4
replies
1.7k
views
problem of GOSemSim R package operation geneSim()
gosemsim
8.8 years ago
bnembarekmarwa
• 0
1
vote
1
reply
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
Guangchuang Yu
★ 1.2k • written 8.8 years ago by
ረ
• 0
0
votes
9
replies
3.2k
views
expired SQLiteConnection in GoSemSim package.
gene ontology
GOSemsim
updated 9.6 years ago by
Paulson, Ariel
▴ 10 • written 9.8 years ago by
anupambtech2007
• 0
0
votes
4
replies
2.2k
views
GOterm semantic similarity with non-reference organism
gosemsim
go
gene ontology
9.8 years ago
cpcantalapiedra
• 0
1
vote
2
replies
2.0k
views
GOSemSim problem for yeast proteins
GOSemSim
yeast
updated 10.0 years ago by
Guangchuang Yu
★ 1.2k • written 10.0 years ago by
horcsct
▴ 10
0
votes
0
replies
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
votes
1
reply
1.6k
views
GOSemSim function, clusterSim throws expired SQLiteConnection error
GO
GOSemSim
GO
GOSemSim
updated 11.2 years ago by
Guangchuang Yu
★ 1.2k • written 11.2 years ago by
Guest User
★ 13k
0
votes
0
replies
1.4k
views
GOSemSim mgeneSim GO.BP calculation time
GO
GOSemSim
GO
GOSemSim
12.4 years ago
Guangchuang Yu
★ 1.2k
0
votes
0
replies
1.1k
views
GOSemSim mgeneSim GO.BP calculation time
GO
GOSemSim
GO
GOSemSim
12.5 years ago
Guest User
★ 13k
0
votes
1
reply
1.6k
views
(pack: GOSemSim) NA semantic similarities between gene clusters
GO
SemSim
GOSemSim
GO
SemSim
GOSemSim
updated 12.6 years ago by
Guangchuang Yu
★ 1.2k • written 12.6 years ago by
Guest User
★ 13k
0
votes
1
reply
1.3k
views
GOSemSim comparison between species
Yeast
GOSemSim
Yeast
GOSemSim
updated 12.7 years ago by
Dan Tenenbaum
★ 8.2k • written 12.7 years ago by
Katharine Coyte
▴ 10
0
votes
1
reply
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
Marc Carlson
★ 7.2k • written 15.4 years ago by
Gang Chen
▴ 20
34 results • Page
1 of 1
Recent ...
Replies
Comment: WGCNA coupled with differential expression analysis: question about baseline mod
by
hetaf16210
• 0
@[slope][1] If feasible, consider conducting both analyses. Start with a pooled analysis to identify broad patterns, then conduct separate …
Comment: DESeq2 adujsted p-value cutoff seemingly not working
by
980linnet
• 0
Stuck on DESeq2 with alpha=.05 for padj cutoff. Can't seem to get the differential expression analysis to stick the landing - it's like try…
Comment: internal error in trio library when trying to use lfmm() in LEA package
by
PW
• 0
>ERROR: unable to open file D://anole_geno.snmf/K1/run1/anole_geno_r1.1.Q. Please, check that the name of the file you provided is correct.…
Comment: DESeq2 adujsted p-value cutoff seemingly not working
by
Guilherme
• 0
Thank you for your answer So the proper way to conduct the analysis is to put the filters in the results() function and later filter the da…
Comment: DiffBind - observation that the default union overlap is actually a gap of 1 bp
by
Ian D.
▴ 70
Please can you comment on this @rory.
Votes
A: how to extract Granges not overlapping with other ganges?
DESeq2 1.20.0 lfcshrink function
A: LIMMA on RT-PCR data
Answer: Efficiently working with HDF5-backed SingleCellExperiments
Efficiently working with HDF5-backed SingleCellExperiments
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ramiro.barrantes
▴ 10
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Vincent J. Carey, Jr.
6.7k
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Gordon Smyth
52k
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