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Showing :
annotationHub
•
reset
0
votes
2
replies
173
views
AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is required
AnnotationHub
Install
updated 8 weeks ago by
shepherl
3.1k • written 8 weeks ago by
nhaus
• 0
0
votes
4
replies
174
views
AnnotationHub
AnnotationHub
8 weeks ago
junliqilinpan
• 0
4
votes
6
replies
363
views
OrgDb (org.Hs.eg.db) missing many EntrezIDs and their Symbols (Compared to Ensembl GRChg8 v103)
AnnotationHub
OrganismDbi
org.Hs.eg.db
updated 10 weeks ago by
Gordon Smyth
45k • written 11 weeks ago by
Nathan
• 0
8
votes
9
replies
727
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 3 months ago by
Hervé Pagès
15k • written 3 months ago by
jon.klonowski
▴ 30
0
votes
2
replies
200
views
AnnotationHub problem
AnnotationHub
4 months ago
Jianxuan
• 0
4
votes
8
replies
528
views
Problem converting transcript to genomic coordinates with Annotation Hub
AnnotationHub
5 months ago • updated 5 days ago
nattzy94
▴ 20
1
vote
3
replies
364
views
How delete the AnnotationHub downloaded datasets
AnnotationHub
updated 7 months ago by
Mike Smith
★ 5.5k • written 7 months ago by
sabermohammdi.1994
• 0
2
votes
10
replies
739
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter
annotationTools
AnnotationHub
AnnotationData
updated 7 months ago by
Guido Hooiveld
★ 3.2k • written 7 months ago by
Javan Okendo
• 0
0
votes
0
replies
157
views
LRBaseDbi error
LRBaseDbi
AnnotationHub
8 months ago
Francois Marchildon
▴ 20
1
vote
2
replies
416
views
Translating Solanum lycopersum gene IDs to ENTREZIDs for GO enrichment analysis using clusterProfiler
OrgDb
Bioconductor
AnnotationHub
clusterProfiler
updated 12 months ago by
Guido Hooiveld
★ 3.2k • written 12 months ago by
ju.ry
• 0
0
votes
1
reply
387
views
News:
Updates to BiocFileCache, AnnotationHub, and ExperimentHub
BiocFileCache
AnnotationHub
ExperimentHub
cache
13 months ago
shepherl
3.1k
0
votes
2
replies
1.2k
views
Convert Agilent Probe ID to gene IDs/Symbols
AnnotationHub
biomaRt
14 months ago
rohitsatyam102
▴ 20
3
votes
8
replies
1.6k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler
AnnotationHub
GO
uniprot
updated 8 weeks ago by
Guido Hooiveld
★ 3.2k • written 15 months ago by
Alberto
• 0
11
votes
13
replies
1.1k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic
AnnotationHub
GenomicRanges
org.Hs.eg.db
18 months ago • updated 15 months ago
rohitsatyam102
▴ 20
8
votes
20
replies
10k
views
ah <- AnnotationHub() Error in UseMethod("filter_"): no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tb…
AnnotationHub
dplyr
18 months ago • updated 10 months ago
georgia.katsoula
▴ 40
3
votes
2
replies
832
views
Issue with AnnotationHub
AnnotationHub
17 months ago
rahnaman
▴ 10
1
vote
2
replies
389
views
How to mimic biomaRt results with AnnotationHub?
biomaRt
AnnotationHub
18 months ago
Ezgi
▴ 30
1
vote
3
replies
346
views
AnnotationHub: failed to load resource name
AnnotationHub
20 months ago
ben.ponv
• 0
4
votes
17
replies
1.0k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt
annotation
Ensembl
annotationHub
updated 20 months ago by
Kevin Blighe
3.5k • written 20 months ago by
Didi
▴ 10
4
votes
2
replies
534
views
News:
ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb
ensembldb
annotation
AnnotationHub
News
21 months ago
Johannes Rainer
★ 1.9k
8
votes
16
replies
1.7k
views
Cannot connect to ExperimentHub server
ExperimentHub
AnnotationHub
SingleR
updated 21 months ago by
shepherl
3.1k • written 21 months ago by
enricoferrero
▴ 610
0
votes
2
replies
375
views
Can't select GO from AnnotationHub orgDB packages
GO.db
AnnotationHub
OrgDB
updated 22 months ago by
James W. MacDonald
59k • written 22 months ago by
Jenny Drnevich
★ 2.0k
0
votes
3
replies
358
views
extracting the genes associated with a specific pathway
pathway
KEGG
annotation
annotationhub
updated 23 months ago by
James W. MacDonald
59k • written 23 months ago by
Bogdan
▴ 640
2
votes
4
replies
530
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub
OrgDb
snapshotDate
updated 2.0 years ago by
shepherl
3.1k • written 2.0 years ago by
Jenny Drnevich
★ 2.0k
2
votes
8
replies
514
views
gene enrichment using enrichGO function throuth annotationHub orgDb
software error
enrichGO
annotationHub
clusterProfiler
Job
updated 2.1 years ago by
James W. MacDonald
59k • written 2.1 years ago by
bnajafpour
• 0
1
vote
5
replies
393
views
AnnotationHub; Error: failed to load resource; Timeout was reached: [annotationhub.bioconductor.org]
annotationhub
updated 2.1 years ago by
shepherl
3.1k • written 2.1 years ago by
dilaik
• 0
0
votes
2
replies
285
views
hg38 tracks for AnnotationHub
annotationhub
2.2 years ago
Michael Love
36k
0
votes
1
reply
289
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub
Shiny
Rstudio
updated 2.2 years ago by
shepherl
3.1k • written 2.2 years ago by
bwiley4
• 0
0
votes
8
replies
1.0k
views
I can't use AnnotationHub()
AnnotationHub
2.4 years ago
755606975
• 0
1
vote
3
replies
1.2k
views
AnnotationHub timeout for Ensembl Mouse GTF
AnnotationHub
Ensembl
Mouse
AnnotationHub Ensembl
2.4 years ago
dmgatti
▴ 10
3
votes
0
replies
393
views
News:
EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
annotation
ensembldb
EnsDb
AnnotationHub
News
2.5 years ago
Johannes Rainer
★ 1.9k
0
votes
2
replies
513
views
how to choose annotation file in AnnotationHub web server
annotation
AnnotationHub
2.5 years ago
15958021290
▴ 10
3
votes
4
replies
456
views
Are AH52264, AH66175, and AH70594 duplicates?
AnnotationHub
updated 2.6 years ago by
shepherl
3.1k • written 2.6 years ago by
Aditya
▴ 140
1
vote
3
replies
382
views
Problem with AnnotationHub after crash during first download of metadata
AnnotationHub
updated 2.7 years ago by
shepherl
3.1k • written 2.7 years ago by
konstantinos.bogias
▴ 10
7
votes
44
replies
1.9k
views
OrgDB download failed via AnnotationHub
annotationhub
orgdb
updated 2.9 years ago by
shepherl
3.1k • written 2.9 years ago by
chirag.parsania
• 0
2
votes
0
replies
415
views
News:
ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata
annotationhub
ensembl
gtf
2bit
News
updated 3.0 years ago by
nguyenlieuduoc
• 0 • written 3.1 years ago by
shepherl
3.1k
1
vote
4
replies
466
views
AnnotationHub Server denied you to change the given directory
annotation
annotationhub
updated 3.0 years ago by
shepherl
3.1k • written 3.0 years ago by
bastien.ducreux
▴ 10
0
votes
11
replies
804
views
AH134 and other AnnotationHub objects unavailable as "defunct"
AnnotationHub
updated 3.1 years ago by
shepherl
3.1k • written 3.1 years ago by
Robert K. Bradley
▴ 40
1
vote
1
reply
472
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
3.1 years ago
wecai
• 0
3
votes
9
replies
2.8k
views
AnnotationHub corrupt database
annotationhub
updated 3.2 years ago by
shepherl
3.1k • written 6.8 years ago by
Koen Van den Berge
▴ 180
0
votes
0
replies
485
views
News:
ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
annotationhub
annotationdata
ensembl
gtf
2bit
News
3.3 years ago
shepherl
3.1k
5
votes
12
replies
1.3k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 5 days ago by
Johannes Rainer
★ 1.9k • written 3.5 years ago by
Guido Hooiveld
★ 3.2k
1
vote
7
replies
585
views
News:
ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
annotationdata
annotationhub
ensembl
gtf
2bit
News
3.6 years ago
shepherl
3.1k
0
votes
5
replies
586
views
annotationhub: data update
annotationhub
updated 3.8 years ago by
shepherl
3.1k • written 3.8 years ago by
Kasper Daniel Hansen
6.5k
0
votes
0
replies
521
views
News:
ensembl 93 gtfs and fasta twobits have been added to AnnotationHub
annotationhub
ensembl
gtf
2bit
annotationdata
News
3.8 years ago
shepherl
3.1k
1
vote
2
replies
878
views
AnnotationHub, force update snapshot date?
annotationhub
updated 3.8 years ago by
shepherl
3.1k • written 3.8 years ago by
Vang Le
▴ 70
5
votes
4
replies
783
views
Eliminating repetitive calls to ExperimentHub
experimenthub
annotationhub
large dataset
4.0 years ago
slinker
▴ 20
0
votes
6
replies
780
views
initialization of AnnotationHub() in version 2.12.0 is problematically verbose
AnnotationHub
updated 4.0 years ago by
Martin Morgan
25k • written 4.0 years ago by
Robert K. Bradley
▴ 40
0
votes
0
replies
603
views
News:
ensembl 92 gtfs and fasta twobits have been added to AnnotationHub
ensembl
gtf
2bit
annotationhub
News
4.1 years ago
shepherl
3.1k
1
vote
0
replies
1.0k
views
News:
ensembl 91 gtfs and fasta twobits have been added to AnnotationHub
annotationhub
ensembl
gtf
2bit
News
4.4 years ago
shepherl
3.1k
50 results • Page
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Comment: performing the differential binding in ChIP-seq
by
Bogdan
▴ 640
Thank you. Yes, DiffBind might be a good choice shall we have replicates per sample. Another choice is MA-norm2. Any other well-tested sug…
Comment: Error using read.ilmn and neqc
by
Gordon Smyth
45k
I edited the title of your question to be more specific.
Answer: Using limma to read Illumina HT-12 v4 data
by
Gordon Smyth
45k
It seems clear that you haven't exported the correct intensity data from GenomeStudio, and I think you recognize that yourself in your ques…
Answer: performing the differential binding in ChIP-seq
by
etiennedanis
• 0
DiffBind https://bioconductor.org/packages/release/bioc/html/DiffBind.html
Comment: Transcript-level differential expression using DESeq2
by
Michael Love
36k
Did you see the part of the vignette where we talk about this? https://bioconductor.org/packages/release/bioc/vignettes/fishpond/inst/doc/…
Votes
Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
Answer: How to best visualize multi-level transcriptomics experiment data?
A: Interpreting results of sample-to-sample PCA/clustering and changing assignment
C: DESeq2 - Differences between plotCounts and normalized counts
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