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Annotationhub
•
reset
0
votes
1
reply
247
views
multiGSEA package in R not appropriately assigning metabolites to pathways?
metaboliteIDmapping
AnnotationHub
multiGSEA
4 months ago • updated 3 months ago
Thomas
• 0
0
votes
11
replies
696
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub
AnnotationForge
Pseudomonas_aeruginosa
updated 5 months ago by
James W. MacDonald
62k • written 5 months ago by
Manmohit
• 0
2
votes
2
replies
356
views
[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19
rtracklayer
AnnotationHub
9 months ago • updated 8 months ago
Lenny186
• 0
0
votes
3
replies
498
views
Differences in ENSEMBL => ENTREZID mapping coverage between org.Hs.eg.db and AnnotationHub resources
AnnotationHub
org.Hs.eg.db
ensembldb
10 months ago • updated 9 months ago
sandmann.t
▴ 70
9
votes
21
replies
13k
views
ah <- AnnotationHub() Error in UseMethod("filter_"): no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tb…
AnnotationHub
dplyr
updated 10 months ago by
SmallChess
▴ 10 • written 2.6 years ago by
georgia.katsoula
▴ 40
0
votes
2
replies
1.2k
views
AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is required
AnnotationHub
Install
updated 14 months ago by
shepherl
3.5k • written 14 months ago by
nhaus
• 0
0
votes
4
replies
587
views
AnnotationHub
AnnotationHub
14 months ago
junliqilinpan
• 0
4
votes
6
replies
1.1k
views
OrgDb (org.Hs.eg.db) missing many EntrezIDs and their Symbols (Compared to Ensembl GRChg8 v103)
AnnotationHub
OrganismDbi
org.Hs.eg.db
updated 14 months ago by
Gordon Smyth
47k • written 15 months ago by
Nathan
• 0
8
votes
9
replies
3.1k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 16 months ago by
Hervé Pagès
16k • written 16 months ago by
jon.klonowski
▴ 40
0
votes
2
replies
542
views
AnnotationHub problem
AnnotationHub
16 months ago
Jianxuan
• 0
4
votes
8
replies
1.1k
views
Problem converting transcript to genomic coordinates with Annotation Hub
AnnotationHub
18 months ago • updated 12 months ago
nattzy94
▴ 20
1
vote
3
replies
722
views
How delete the AnnotationHub downloaded datasets
AnnotationHub
updated 19 months ago by
Mike Smith
★ 6.0k • written 19 months ago by
sabermohammdi.1994
• 0
2
votes
10
replies
1.5k
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter
annotationTools
AnnotationHub
AnnotationData
updated 19 months ago by
Guido Hooiveld
★ 3.6k • written 19 months ago by
Javan Okendo
• 0
0
votes
0
replies
359
views
LRBaseDbi error
LRBaseDbi
AnnotationHub
21 months ago
Francois Marchildon
▴ 20
1
vote
2
replies
825
views
Translating Solanum lycopersum gene IDs to ENTREZIDs for GO enrichment analysis using clusterProfiler
OrgDb
Bioconductor
AnnotationHub
clusterProfiler
updated 2.1 years ago by
Guido Hooiveld
★ 3.6k • written 2.1 years ago by
ju.ry
• 0
0
votes
1
reply
707
views
News:
Updates to BiocFileCache, AnnotationHub, and ExperimentHub
BiocFileCache
AnnotationHub
ExperimentHub
cache
2.1 years ago
shepherl
3.5k
0
votes
3
replies
2.8k
views
Convert Agilent Probe ID to gene IDs/Symbols
AnnotationHub
biomaRt
updated 9 months ago by
alvea2008667
• 0 • written 2.2 years ago by
rohitsatyam102
▴ 20
3
votes
8
replies
3.0k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler
AnnotationHub
GO
uniprot
updated 14 months ago by
Guido Hooiveld
★ 3.6k • written 2.3 years ago by
Alberto
• 0
11
votes
13
replies
2.3k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic
AnnotationHub
GenomicRanges
org.Hs.eg.db
2.5 years ago • updated 2.3 years ago
rohitsatyam102
▴ 20
3
votes
2
replies
1.3k
views
Issue with AnnotationHub
AnnotationHub
2.5 years ago
rahnaman
▴ 10
1
vote
2
replies
757
views
How to mimic biomaRt results with AnnotationHub?
biomaRt
AnnotationHub
2.5 years ago
Ezgi
▴ 30
1
vote
3
replies
574
views
AnnotationHub: failed to load resource name
AnnotationHub
2.7 years ago
ben.ponv
• 0
4
votes
17
replies
1.6k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt
annotation
Ensembl
annotationHub
updated 2.7 years ago by
Kevin Blighe
3.8k • written 2.7 years ago by
Didi
▴ 10
4
votes
2
replies
1.0k
views
News:
ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb
ensembldb
annotation
AnnotationHub
News
2.8 years ago
Johannes Rainer
★ 2.0k
8
votes
16
replies
3.1k
views
Cannot connect to ExperimentHub server
ExperimentHub
AnnotationHub
SingleR
updated 2.8 years ago by
shepherl
3.5k • written 2.8 years ago by
enricoferrero
▴ 660
0
votes
2
replies
775
views
Can't select GO from AnnotationHub orgDB packages
GO.db
AnnotationHub
OrgDB
updated 2.9 years ago by
James W. MacDonald
62k • written 2.9 years ago by
Jenny Drnevich
★ 2.0k
0
votes
3
replies
684
views
extracting the genes associated with a specific pathway
pathway
KEGG
annotation
annotationhub
updated 3.0 years ago by
James W. MacDonald
62k • written 3.0 years ago by
Bogdan
▴ 660
3
votes
6
replies
1.3k
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub
OrgDb
snapshotDate
updated 10 months ago by
shepherl
3.5k • written 3.0 years ago by
Jenny Drnevich
★ 2.0k
2
votes
8
replies
943
views
gene enrichment using enrichGO function throuth annotationHub orgDb
software error
enrichGO
annotationHub
clusterProfiler
Job
updated 3.1 years ago by
James W. MacDonald
62k • written 3.1 years ago by
bnajafpour
• 0
1
vote
5
replies
910
views
AnnotationHub; Error: failed to load resource; Timeout was reached: [annotationhub.bioconductor.org]
annotationhub
updated 3.2 years ago by
shepherl
3.5k • written 3.2 years ago by
dilaik
• 0
0
votes
2
replies
601
views
hg38 tracks for AnnotationHub
annotationhub
3.2 years ago
Michael Love
40k
0
votes
1
reply
533
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub
Shiny
Rstudio
updated 3.2 years ago by
shepherl
3.5k • written 3.2 years ago by
bwiley4
• 0
0
votes
8
replies
1.5k
views
I can't use AnnotationHub()
AnnotationHub
3.4 years ago
755606975
• 0
1
vote
3
replies
1.8k
views
AnnotationHub timeout for Ensembl Mouse GTF
AnnotationHub
Ensembl
Mouse
AnnotationHub Ensembl
3.5 years ago
dmgatti
▴ 10
3
votes
0
replies
698
views
News:
EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
annotation
ensembldb
EnsDb
AnnotationHub
News
3.5 years ago
Johannes Rainer
★ 2.0k
2
votes
2
replies
865
views
how to choose annotation file in AnnotationHub web server
annotation
AnnotationHub
3.5 years ago
15958021290
▴ 10
3
votes
4
replies
756
views
Are AH52264, AH66175, and AH70594 duplicates?
AnnotationHub
updated 3.6 years ago by
shepherl
3.5k • written 3.6 years ago by
Aditya
▴ 160
1
vote
3
replies
571
views
Problem with AnnotationHub after crash during first download of metadata
AnnotationHub
updated 3.7 years ago by
shepherl
3.5k • written 3.8 years ago by
konstantinos.bogias
▴ 10
7
votes
44
replies
3.2k
views
OrgDB download failed via AnnotationHub
annotationhub
orgdb
updated 3.9 years ago by
shepherl
3.5k • written 3.9 years ago by
chirag.parsania
• 0
2
votes
0
replies
615
views
News:
ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata
annotationhub
ensembl
gtf
2bit
News
updated 4.1 years ago by
nguyenlieuduoc
• 0 • written 4.1 years ago by
shepherl
3.5k
1
vote
4
replies
741
views
AnnotationHub Server denied you to change the given directory
annotation
annotationhub
updated 4.1 years ago by
shepherl
3.5k • written 4.1 years ago by
bastien.ducreux
▴ 10
0
votes
11
replies
1.2k
views
AH134 and other AnnotationHub objects unavailable as "defunct"
AnnotationHub
updated 4.1 years ago by
shepherl
3.5k • written 4.1 years ago by
Robert K. Bradley
▴ 40
1
vote
1
reply
746
views
The total genes items (e.g. ENTREZ ID, SYMBOL) in OrgDb (Salmo salar; [["AH66207"]]) is just half the gene number in NCBI ?!
Annotationhub
Annotationdb
profiler
annotationdbi
4.1 years ago
wecai
• 0
3
votes
9
replies
3.2k
views
AnnotationHub corrupt database
annotationhub
updated 4.2 years ago by
shepherl
3.5k • written 7.8 years ago by
Koen Van den Berge
▴ 180
0
votes
0
replies
692
views
News:
ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
annotationhub
annotationdata
ensembl
gtf
2bit
News
4.3 years ago
shepherl
3.5k
5
votes
19
replies
2.6k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 7 months ago by
Johannes Rainer
★ 2.0k • written 4.5 years ago by
Guido Hooiveld
★ 3.6k
1
vote
7
replies
782
views
News:
ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
annotationdata
annotationhub
ensembl
gtf
2bit
News
4.6 years ago
shepherl
3.5k
0
votes
5
replies
825
views
annotationhub: data update
annotationhub
updated 4.8 years ago by
shepherl
3.5k • written 4.8 years ago by
Kasper Daniel Hansen
6.5k
0
votes
0
replies
687
views
News:
ensembl 93 gtfs and fasta twobits have been added to AnnotationHub
annotationhub
ensembl
gtf
2bit
annotationdata
News
4.8 years ago
shepherl
3.5k
1
vote
2
replies
1.2k
views
AnnotationHub, force update snapshot date?
annotationhub
updated 4.9 years ago by
shepherl
3.5k • written 4.9 years ago by
Vang Le
▴ 80
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Comment: Normalized counts from LRT or Wald test?
by
sneha108ss
• 0
That is great to know! Thank you
Comment: Installing densvis on a Singularity container
by
alan.ocallaghan
▴ 120
Do you have gfortran installed? eg [this installation package][1] [1]: https://github.com/fxcoudert/gfortran-for-macOS
Comment: Installing densvis on a Singularity container
by
azp0136
• 0
I get the same error when I try to install densvis in R with `BiocManager::install("densvis")` and I have no idea how to solve this problem…
Comment: Error in DGEList(counts = cnt, group = group) : non-numeric values found in c
by
Luis
• 0
Thank you so much!
Comment: Error in DGEList(counts = cnt, group = group) : non-numeric values found in c
by
Luis
• 0
I understand, thank you very much for all the support and collaboration!
Votes
How to create "trait data" file for WGCNA
Comment: Visualization of negative log CPM values
Answer: Extracting fitted expression matrix from Limma
Answer: DESeq2 or edgeR for Presence and Absence of Proteins
Comment: Visualization of negative log CPM values
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