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Annotationhub
•
reset
11
votes
13
replies
3.9k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic
AnnotationHub
GenomicRanges
org.Hs.eg.db
3.3 years ago • updated 3.2 years ago
rohitsatyam102
▴ 20
9
votes
11
replies
5.5k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 16 days ago by
shepherl
3.8k • written 2.2 years ago by
jon.klonowski
▴ 40
9
votes
21
replies
14k
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 20 months ago by
SmallChess
▴ 10 • written 3.4 years ago by
georgia.katsoula
▴ 40
8
votes
4
replies
4.3k
views
Tutorial:
Epigenomics RoadMap Project files now accessible via AnnotationHub
AnnotationHub
Epigenomics
BigData
RoadMap Project
NIH
Tutorial
updated 6.9 years ago by
vanesa_1230
• 0 • written 8.8 years ago by
Sonali Arora
▴ 390
8
votes
16
replies
5.9k
views
Cannot connect to ExperimentHub server
ExperimentHub
AnnotationHub
SingleR
updated 3.6 years ago by
shepherl
3.8k • written 3.6 years ago by
enricoferrero
▴ 660
7
votes
44
replies
5.3k
views
OrgDB download failed via AnnotationHub
annotationhub
orgdb
updated 4.7 years ago by
shepherl
3.8k • written 4.8 years ago by
chirag.parsania
• 0
7
votes
11
replies
6.3k
views
Error in sqliteSendQuery(conn, statement): error in statement: no such table: c.probes
edgeR
limma
annotationhub
kegga
annotationdbi
updated 7.7 years ago by
cagenet34
▴ 20 • written 8.0 years ago by
Rinaldo Bertossa
▴ 20
7
votes
32
replies
5.1k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 5 weeks ago by
Emmi
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
6
votes
9
replies
4.1k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
updated 16 days ago by
Melissa
• 0 • written 5 months ago by
shepherl
3.8k
5
votes
2
replies
1.2k
views
AnnotationHub: two broad peaks from same url are not the same
annotationhub
bugs
encode
bed
7.3 years ago
wcstcyx
▴ 30
5
votes
4
replies
1.3k
views
Eliminating repetitive calls to ExperimentHub
experimenthub
annotationhub
large dataset
5.9 years ago
slinker
▴ 20
5
votes
11
replies
2.5k
views
Certificate problem with ExperimentHub / AnnotationHub
software error
curatedmetagenomicdata
annotationhub
experimenthub
updated 7.3 years ago by
Levi Waldron
★ 1.1k • written 7.3 years ago by
morganx
▴ 10
4
votes
3
replies
1.9k
views
Error installing AnnotationHub on Fedora
Annotationhub
curl
httr
fedora
updated 7.9 years ago by
anastazie.d
▴ 30 • written 8.6 years ago by
barashe
▴ 10
4
votes
8
replies
1.7k
views
Problem converting transcript to genomic coordinates with Annotation Hub
AnnotationHub
2.3 years ago • updated 22 months ago
nattzy94
▴ 20
4
votes
17
replies
2.4k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt
annotation
Ensembl
annotationHub
updated 3.6 years ago by
Kevin Blighe
★ 3.9k • written 3.6 years ago by
Didi
▴ 10
4
votes
7
replies
1.5k
views
AnnotationHub and ExperimentHub make "~" directory in my home
annotationhub
experimenthub
updated 7.6 years ago by
Valerie Obenchain
★ 6.8k • written 7.6 years ago by
Michael Love
41k
4
votes
10
replies
1.2k
views
Suggestion: spinning wheel for AnnotationHub
annotationhub
updated 6.5 years ago by
shepherl
3.8k • written 6.6 years ago by
Michael Love
41k
4
votes
1
reply
3.7k
views
getting the longest transcript by gene from Refseq
refseq
annotationhub
updated 8.5 years ago by
Martin Morgan
25k • written 8.5 years ago by
dalloliogm
▴ 50
4
votes
2
replies
1.6k
views
News:
ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb
ensembldb
annotation
AnnotationHub
News
3.6 years ago
Johannes Rainer
★ 2.0k
4
votes
6
replies
2.2k
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
3
votes
3
replies
1.4k
views
Broken AnnotationHub resource (AH25517 | wgEncodeOpenChromDnaseGm12878Pk.narrowPeak.gz)
annotationhub
encode
updated 8.0 years ago by
Valerie Obenchain
★ 6.8k • written 8.0 years ago by
Peter Hickey
▴ 670
3
votes
4
replies
1.1k
views
Are AH52264, AH66175, and AH70594 duplicates?
AnnotationHub
updated 4.4 years ago by
shepherl
3.8k • written 4.4 years ago by
Aditya
▴ 160
3
votes
13
replies
2.6k
views
Org.db: why a supposed unique key (ID) has multiple entries?
annotationhub
organismdb
orgdb
unsupported organisms
updated 8.2 years ago by
Valerie Obenchain
★ 6.8k • written 8.2 years ago by
Guido Hooiveld
★ 3.9k
3
votes
4
replies
1.1k
views
Annotation hub and clusterProfiler errors
clusterProfiler
Annotationhub
updated 5 months ago by
Guido Hooiveld
★ 3.9k • written 5 months ago by
BS
• 0
3
votes
2
replies
1.9k
views
Issue with AnnotationHub
AnnotationHub
3.3 years ago
rahnaman
▴ 10
3
votes
9
replies
3.9k
views
AnnotationHub corrupt database
annotationhub
updated 5.0 years ago by
shepherl
3.8k • written 8.7 years ago by
Koen Van den Berge
▴ 180
3
votes
11
replies
4.7k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler
AnnotationHub
GO
uniprot
updated 7 weeks ago by
Guido Hooiveld
★ 3.9k • written 3.2 years ago by
Alberto
• 0
3
votes
2
replies
1.6k
views
AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
annotationhub
roadmap project
rpkm
data.frame
7.5 years ago • updated 7.4 years ago
wcstcyx
▴ 30
3
votes
6
replies
2.1k
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub
OrgDb
snapshotDate
updated 20 months ago by
shepherl
3.8k • written 3.9 years ago by
Jenny Drnevich
★ 2.0k
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
4.3 years ago
Johannes Rainer
★ 2.0k
3
votes
1
reply
1.3k
views
AnnotationHub: confusing pValue/qValue for (some) Roadmap records
roadmap project
annotationhub
epigenomics
big data
updated 7.9 years ago by
Valerie Obenchain
★ 6.8k • written 7.9 years ago by
kevin.rue
▴ 350
2
votes
2
replies
1.9k
views
Normal Patient Samples from GSE62944
GSE62944
annotationhub
differentialexpression
updated 8.0 years ago by
Sonali Arora
▴ 390 • written 8.0 years ago by
hamda.binte.ajmal
• 0
2
votes
2
replies
1.2k
views
how to choose annotation file in AnnotationHub web server
annotation
AnnotationHub
4.4 years ago
15958021290
▴ 10
2
votes
1
reply
283
views
clusterProfiler, AnnotationHub, and discrepancies in GO Terms
Atlanticsalmon
clusterPro
Salmosalar
AnnotationHub
GeneOntology
updated 27 days ago by
Michael Love
41k • written 28 days ago by
Filipe
• 0
2
votes
8
replies
1.7k
views
Problem fetching resources from AnnotationHub, error 403
AnnotationHub
updated 8.4 years ago by
Valerie Obenchain
★ 6.8k • written 8.4 years ago by
Johannes Rainer
★ 2.0k
2
votes
0
replies
942
views
News:
ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata
annotationhub
ensembl
gtf
2bit
News
updated 4.9 years ago by
nguyenlieuduoc
• 0 • written 4.9 years ago by
shepherl
3.8k
2
votes
0
replies
3.3k
views
News:
Gencode GFF3 and FASTA files now available via AnnotationHub
AnnotationHub
Gencode
GFF3
FASTA
News
8.6 years ago
Sonali Arora
▴ 390
2
votes
12
replies
2.3k
views
AnnotationHub-cant extract database
annotationhub
updated 7.0 years ago by
Valerie Obenchain
★ 6.8k • written 7.0 years ago by
ecpierce
• 0
2
votes
10
replies
2.2k
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter
annotationTools
AnnotationHub
AnnotationData
updated 2.4 years ago by
Guido Hooiveld
★ 3.9k • written 2.4 years ago by
Javan Okendo
• 0
2
votes
28
replies
4.2k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub
AnnotationForge
Pseudomonas_aeruginosa
updated 4 months ago by
James W. MacDonald
65k • written 15 months ago by
Manmohit
▴ 10
2
votes
3
replies
1.3k
views
Why No Uniprot information for some other organisms in AnnotationHub?
hub
annotationhub
updated 3.2 years ago by
shepherl
3.8k • written 7.5 years ago by
wssdandan2009
• 0
2
votes
12
replies
3.1k
views
Error: failed to load 'AnnotationHub' resource
biomart
annotationhub
updated 8.4 years ago by
Martin Morgan
25k • written 8.4 years ago by
borowczak.marc
▴ 10
2
votes
6
replies
1.4k
views
R getting "stuck" with RoadMap resource retrieval through AnnotationHub
roadmap project
annotationhub
6.9 years ago
vanesa_1230
• 0
2
votes
0
replies
843
views
News:
ensembl 89 gtfs and fasta twobits have been added to AnnotationHub
bioconductor
annotationhub
ensembl89
News
6.8 years ago
shepherl
3.8k
2
votes
8
replies
1.6k
views
gene enrichment using enrichGO function throuth annotationHub orgDb
software error
enrichGO
annotationHub
clusterProfiler
Job
updated 3.9 years ago by
James W. MacDonald
65k • written 3.9 years ago by
bnajafpour
• 0
2
votes
2
replies
715
views
[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19
rtracklayer
AnnotationHub
19 months ago • updated 18 months ago
Lenny186
• 0
1
vote
3
replies
3.4k
views
Problem using display() function on RStudio
display
rstudio
annotationhub
updated 8.6 years ago by
James W. MacDonald
65k • written 8.6 years ago by
barashe
▴ 10
1
vote
4
replies
1.2k
views
AnnotationHub Server denied you to change the given directory
annotation
annotationhub
updated 4.9 years ago by
shepherl
3.8k • written 4.9 years ago by
bastien.ducreux
▴ 10
1
vote
3
replies
2.0k
views
annotation of SV (Structural Variants)
variantannotation
annotationhub
7.0 years ago
Bogdan
▴ 670
1
vote
1
reply
1.0k
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
1 of 1
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Replies
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
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Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
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50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
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65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
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