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AnnotationHub
•
reset
6
votes
12
replies
4.7k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 4 days ago
shepherl
3.8k
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 22 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
0
votes
6
replies
311
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 15 days ago by
Tim Peters
▴ 170 • written 24 days ago by
s.malik
• 0
2
votes
1
reply
323
views
clusterProfiler, AnnotationHub, and discrepancies in GO Terms
Atlanticsalmon
clusterPro
Salmosalar
AnnotationHub
GeneOntology
updated 8 weeks ago by
Michael Love
41k • written 8 weeks ago by
Filipe
• 0
0
votes
0
replies
156
views
Annotatr Duplicate Entries
annotatr
AnnotationHub
3 months ago
hayleyw
• 0
2
votes
28
replies
4.3k
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
65k • written 16 months ago by
Manmohit
▴ 10
3
votes
4
replies
1.2k
views
Annotation hub and clusterProfiler errors
clusterProfiler
Annotationhub
updated 6 months ago by
Guido Hooiveld
★ 3.9k • written 6 months ago by
BS
• 0
1
vote
2
replies
552
views
AnnotationHub data for Mus musculus seems to be missing, while previously it was there
tximeta
AnnotationHub
AnnotationHubData
6 months ago
Thon
• 0
0
votes
1
reply
689
views
multiGSEA package in R not appropriately assigning metabolites to pathways?
metaboliteIDmapping
AnnotationHub
multiGSEA
15 months ago • updated 14 months ago
Thomas
• 0
2
votes
2
replies
756
views
[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19
rtracklayer
AnnotationHub
20 months ago • updated 19 months ago
Lenny186
• 0
0
votes
3
replies
1.2k
views
Differences in ENSEMBL => ENTREZID mapping coverage between org.Hs.eg.db and AnnotationHub resources
AnnotationHub
org.Hs.eg.db
ensembldb
21 months ago • updated 20 months ago
sandmann.t
▴ 70
9
votes
21
replies
15k
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 21 months ago by
SmallChess
▴ 10 • written 3.5 years ago by
georgia.katsoula
▴ 40
0
votes
2
replies
1.9k
views
AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is required
AnnotationHub
Install
updated 2.1 years ago by
shepherl
3.8k • written 2.1 years ago by
nhaus
▴ 30
0
votes
4
replies
1.2k
views
AnnotationHub
AnnotationHub
2.1 years ago
junliqilinpan
• 0
4
votes
6
replies
2.3k
views
OrgDb (org.Hs.eg.db) missing many EntrezIDs and their Symbols (Compared to Ensembl GRChg8 v103)
AnnotationHub
OrganismDbi
org.Hs.eg.db
updated 2.1 years ago by
Gordon Smyth
50k • written 2.1 years ago by
Nathan
• 0
9
votes
11
replies
5.7k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 6 weeks ago by
shepherl
3.8k • written 2.3 years ago by
jon.klonowski
▴ 40
0
votes
2
replies
963
views
AnnotationHub problem
AnnotationHub
2.3 years ago
Jianxuan
• 0
4
votes
8
replies
1.9k
views
Problem converting transcript to genomic coordinates with Annotation Hub
AnnotationHub
2.4 years ago • updated 23 months ago
nattzy94
▴ 20
1
vote
3
replies
1.1k
views
How delete the AnnotationHub downloaded datasets
AnnotationHub
updated 2.5 years ago by
Mike Smith
★ 6.5k • written 2.5 years ago by
sabermohammdi.1994
• 0
2
votes
10
replies
2.3k
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter
annotationTools
AnnotationHub
AnnotationData
updated 2.5 years ago by
Guido Hooiveld
★ 3.9k • written 2.5 years ago by
Javan Okendo
• 0
0
votes
0
replies
599
views
LRBaseDbi error
LRBaseDbi
AnnotationHub
2.6 years ago
Francois Marchildon
▴ 20
1
vote
2
replies
1.4k
views
Translating Solanum lycopersum gene IDs to ENTREZIDs for GO enrichment analysis using clusterProfiler
OrgDb
Bioconductor
AnnotationHub
clusterProfiler
updated 3.0 years ago by
Guido Hooiveld
★ 3.9k • written 3.0 years ago by
ju.ry
• 0
0
votes
1
reply
1.1k
views
News:
Updates to BiocFileCache, AnnotationHub, and ExperimentHub
BiocFileCache
AnnotationHub
ExperimentHub
cache
3.1 years ago
shepherl
3.8k
0
votes
3
replies
4.2k
views
Convert Agilent Probe ID to gene IDs/Symbols
AnnotationHub
biomaRt
updated 20 months ago by
alvea2008667
• 0 • written 3.1 years ago by
rohitsatyam102
▴ 20
3
votes
11
replies
4.9k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler
AnnotationHub
GO
uniprot
updated 11 weeks ago by
Guido Hooiveld
★ 3.9k • written 3.2 years ago by
Alberto
• 0
11
votes
13
replies
4.0k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic
AnnotationHub
GenomicRanges
org.Hs.eg.db
3.4 years ago • updated 3.2 years ago
rohitsatyam102
▴ 20
3
votes
2
replies
2.0k
views
Issue with AnnotationHub
AnnotationHub
3.4 years ago
rahnaman
▴ 10
1
vote
2
replies
1.1k
views
How to mimic biomaRt results with AnnotationHub?
biomaRt
AnnotationHub
3.5 years ago
Ezgi
▴ 60
1
vote
3
replies
999
views
AnnotationHub: failed to load resource name
AnnotationHub
3.7 years ago
ben.ponv
• 0
4
votes
17
replies
2.5k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt
annotation
Ensembl
annotationHub
updated 3.7 years ago by
Kevin Blighe
★ 3.9k • written 3.7 years ago by
Didi
▴ 10
4
votes
2
replies
1.6k
views
News:
ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb
ensembldb
annotation
AnnotationHub
News
3.7 years ago
Johannes Rainer
★ 2.0k
8
votes
16
replies
6.2k
views
Cannot connect to ExperimentHub server
ExperimentHub
AnnotationHub
SingleR
updated 3.7 years ago by
shepherl
3.8k • written 3.7 years ago by
enricoferrero
▴ 660
0
votes
2
replies
1.3k
views
Can't select GO from AnnotationHub orgDB packages
GO.db
AnnotationHub
OrgDB
updated 3.8 years ago by
James W. MacDonald
65k • written 3.8 years ago by
Jenny Drnevich
★ 2.0k
0
votes
3
replies
1.1k
views
extracting the genes associated with a specific pathway
pathway
KEGG
annotation
annotationhub
updated 3.9 years ago by
James W. MacDonald
65k • written 3.9 years ago by
Bogdan
▴ 670
3
votes
6
replies
2.2k
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub
OrgDb
snapshotDate
updated 21 months ago by
shepherl
3.8k • written 3.9 years ago by
Jenny Drnevich
★ 2.0k
2
votes
8
replies
1.6k
views
gene enrichment using enrichGO function throuth annotationHub orgDb
software error
enrichGO
annotationHub
clusterProfiler
Job
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
bnajafpour
• 0
1
vote
5
replies
1.6k
views
AnnotationHub; Error: failed to load resource; Timeout was reached: [annotationhub.bioconductor.org]
annotationhub
updated 4.1 years ago by
shepherl
3.8k • written 4.1 years ago by
dilaik
• 0
0
votes
2
replies
956
views
hg38 tracks for AnnotationHub
annotationhub
4.1 years ago
Michael Love
41k
0
votes
1
reply
926
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub
Shiny
Rstudio
updated 4.2 years ago by
shepherl
3.8k • written 4.2 years ago by
bwiley4
• 0
0
votes
8
replies
2.7k
views
I can't use AnnotationHub()
AnnotationHub
4.3 years ago
755606975
• 0
1
vote
3
replies
2.3k
views
AnnotationHub timeout for Ensembl Mouse GTF
AnnotationHub
Ensembl
Mouse
AnnotationHub Ensembl
4.4 years ago
dmgatti
▴ 10
3
votes
0
replies
1.0k
views
News:
EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
annotation
ensembldb
EnsDb
AnnotationHub
News
4.4 years ago
Johannes Rainer
★ 2.0k
2
votes
2
replies
1.2k
views
how to choose annotation file in AnnotationHub web server
annotation
AnnotationHub
4.4 years ago
15958021290
▴ 10
3
votes
4
replies
1.1k
views
Are AH52264, AH66175, and AH70594 duplicates?
AnnotationHub
updated 4.5 years ago by
shepherl
3.8k • written 4.5 years ago by
Aditya
▴ 160
1
vote
3
replies
1.0k
views
Problem with AnnotationHub after crash during first download of metadata
AnnotationHub
updated 4.6 years ago by
shepherl
3.8k • written 4.7 years ago by
konstantinos.bogias
▴ 10
7
votes
44
replies
5.4k
views
OrgDB download failed via AnnotationHub
annotationhub
orgdb
updated 4.8 years ago by
shepherl
3.8k • written 4.9 years ago by
chirag.parsania
• 0
2
votes
0
replies
980
views
News:
ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata
annotationhub
ensembl
gtf
2bit
News
updated 5.0 years ago by
nguyenlieuduoc
• 0 • written 5.0 years ago by
shepherl
3.8k
1
vote
4
replies
1.2k
views
AnnotationHub Server denied you to change the given directory
annotation
annotationhub
updated 5.0 years ago by
shepherl
3.8k • written 5.0 years ago by
bastien.ducreux
▴ 10
0
votes
11
replies
1.8k
views
AH134 and other AnnotationHub objects unavailable as "defunct"
AnnotationHub
updated 5.0 years ago by
shepherl
3.8k • written 5.0 years ago by
Robert K. Bradley
▴ 40
1
vote
1
reply
1.1k
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
5.0 years ago
wecai
• 0
50 results • Page
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Recent ...
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Comment: Math expression in shapeCustom legend in EnhancedVolcano
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pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
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41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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